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Conserved domains on  [gi|15229763|ref|NP_189961|]
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RING/U-box protein with C6HC-type zinc finger domain-containing protein [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
BRcat_RBR_unk cd22582
BRcat domain found in an uncharacterized subfamily of RBR proteins; This subfamily contains ...
236-294 1.14e-24

BRcat domain found in an uncharacterized subfamily of RBR proteins; This subfamily contains uncharacterized members of the RBR family, including Arabidopsis thaliana mutator-like transposase, hypothetical protein F9K21.90, and hypothetical protein T16H5.30. The RBR family of RING-type E3 ligases are characterized by containing a RBR domain, which was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. It is composed of an extended RING domain (RING1) followed by an in-between RING (IBR) domain and the catalytic domain, which is structurally an IBR domain but is commonly designated RING2. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently, where the IBR and RING2 domains have been renamed as BRcat and Rcat domains, respectively. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. The BRcat domain adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes.


:

Pssm-ID: 439033  Cd Length: 56  Bit Score: 94.74  E-value: 1.14e-24
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15229763 236 VAERVYCPNPRCSGLMSKTELStstEEDVSTRTCCVKCGEPFCINCKVPWHSNLSCDDY 294
Cdd:cd22582   1 VSERVYCPNPDCSALMSKDELL---EAEDDTPRECPKCRRLFCARCKVPWHAGLSCAEY 56
RNase_H_like super family cl14782
Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of ...
26-139 1.33e-16

Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8; Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions.


The actual alignment was detected with superfamily member pfam13456:

Pssm-ID: 449355 [Multi-domain]  Cd Length: 123  Bit Score: 74.99  E-value: 1.33e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229763    26 SQLLAGFGVAIFDQDDKLLFQMKRPIHGSdITVLEAELTALKQGLTETMKLGLDRISICCDHDHIYELVMGRStPEQDNI 105
Cdd:pfam13456   9 DSGLAGAGVVIRDPNGNVLLAGQKKLGPG-ASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRS-PKQSKL 86
                          90       100       110
                  ....*....|....*....|....*....|....
gi 15229763   106 AMLMNDVQRMRQQLRYSNPILVTRDQISFAYKLA 139
Cdd:pfam13456  87 ANLLDEIRKLLKRFESVSFEHIPREQNRVADTLA 120
RING_Ubox super family cl17238
RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger ...
154-205 2.44e-06

RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type RING fingers are closely related to RING-HC fingers. In contrast, C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type RING fingers are more closely related to RING-H2 fingers. However, not all RING finger-containing proteins display regular RING finger features, and the RING finger family has turned out to be multifarious. The degenerate RING fingers of the Siz/PIAS RING (SP-RING) family proteins and sporulation protein RMD5, are characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues. They bind only one Zn2+ ion. On the other hand, the RING fingers of the human APC11 and RBX1 proteins can bind a third Zn atom since they harbor four additional Zn ligands. U-box is a modified form of the RING finger domain that lacks metal chelating Cys and His residues. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms. RING finger/U-box-containing proteins are a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enable efficient transfer of ubiquitin from E2 to the substrates.


The actual alignment was detected with superfamily member cd16628:

Pssm-ID: 473075  Cd Length: 59  Bit Score: 44.22  E-value: 2.44e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15229763 154 TCSICFNNVLeAEKMFSVAICGHQFCVECVKHYIEVKLLEGGVP--RCLDYQCE 205
Cdd:cd16628   7 TCNICFLDKL-GSECMYFKDCGHVYCKECLKEYFEVQIRDGNVTslNCPEPKCA 59
BRcat_Rcat_RBR super family cl45895
BRcat (benign-catalytic) and Rcat (required-for-catalysis) domains, part of the RBR ...
316-339 5.09e-05

BRcat (benign-catalytic) and Rcat (required-for-catalysis) domains, part of the RBR (RING1-BRcat-Rcat) domain; The RBR family of RING-type E3 ligases are characterized by containing an RBR (RING1-BRcat-Rcat) domain, which was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. It is composed of an extended RING domain (RING1) followed by an in-between RING (IBR) domain and the catalytic domain, which is structurally an IBR domain but is commonly designated as RING2. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBRs has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis), where the IBR and RING2 domains have been renamed as BRcat and Rcat domains, respectively. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. The BRcat domain adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes.


The actual alignment was detected with superfamily member cd22584:

Pssm-ID: 459240  Cd Length: 37  Bit Score: 39.90  E-value: 5.09e-05
                        10        20
                ....*....|....*....|....
gi 15229763 316 KWSQCAKCQHMIARIEGCNVIICR 339
Cdd:cd22584   1 GWRRCPQCGHMVELSEGCNHMTCR 24
 
Name Accession Description Interval E-value
BRcat_RBR_unk cd22582
BRcat domain found in an uncharacterized subfamily of RBR proteins; This subfamily contains ...
236-294 1.14e-24

BRcat domain found in an uncharacterized subfamily of RBR proteins; This subfamily contains uncharacterized members of the RBR family, including Arabidopsis thaliana mutator-like transposase, hypothetical protein F9K21.90, and hypothetical protein T16H5.30. The RBR family of RING-type E3 ligases are characterized by containing a RBR domain, which was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. It is composed of an extended RING domain (RING1) followed by an in-between RING (IBR) domain and the catalytic domain, which is structurally an IBR domain but is commonly designated RING2. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently, where the IBR and RING2 domains have been renamed as BRcat and Rcat domains, respectively. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. The BRcat domain adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes.


Pssm-ID: 439033  Cd Length: 56  Bit Score: 94.74  E-value: 1.14e-24
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15229763 236 VAERVYCPNPRCSGLMSKTELStstEEDVSTRTCCVKCGEPFCINCKVPWHSNLSCDDY 294
Cdd:cd22582   1 VSERVYCPNPDCSALMSKDELL---EAEDDTPRECPKCRRLFCARCKVPWHAGLSCAEY 56
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
26-139 1.33e-16

Reverse transcriptase-like; This domain is found in plants and appears to be part of a retrotransposon.


Pssm-ID: 433223 [Multi-domain]  Cd Length: 123  Bit Score: 74.99  E-value: 1.33e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229763    26 SQLLAGFGVAIFDQDDKLLFQMKRPIHGSdITVLEAELTALKQGLTETMKLGLDRISICCDHDHIYELVMGRStPEQDNI 105
Cdd:pfam13456   9 DSGLAGAGVVIRDPNGNVLLAGQKKLGPG-ASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRS-PKQSKL 86
                          90       100       110
                  ....*....|....*....|....*....|....
gi 15229763   106 AMLMNDVQRMRQQLRYSNPILVTRDQISFAYKLA 139
Cdd:pfam13456  87 ANLLDEIRKLLKRFESVSFEHIPREQNRVADTLA 120
IBR smart00647
In Between Ring fingers; the domains occurs between pairs og RING fingers
225-291 3.04e-16

In Between Ring fingers; the domains occurs between pairs og RING fingers


Pssm-ID: 214763 [Multi-domain]  Cd Length: 64  Bit Score: 72.06  E-value: 3.04e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15229763    225 WKQRIEEELILV-AERVYCPNPRCSGLMSKTElststeEDVSTRTCCVKCGEPFCINCKVPWHSNLSC 291
Cdd:smart00647   3 YERLLLESYVESnPDLKWCPAPDCSAAIIVTE------EEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64
IBR pfam01485
IBR domain, a half RING-finger domain; The IBR (In Between Ring fingers) domain is often found ...
226-291 4.75e-09

IBR domain, a half RING-finger domain; The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (pfam00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain. Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organizms. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. The ubiquitin ligase Parkin is an RBR family protein whose mutations are involved in forms of familial Parkinson's disease.


Pssm-ID: 460227  Cd Length: 65  Bit Score: 52.16  E-value: 4.75e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15229763   226 KQRIEEELILVAERVYCPNPRCSGLMSKTELSTSTEedvstRTCCVKCGEPFCINCKVPWHSNLSC 291
Cdd:pfam01485   5 KLLLKSYVESDPNLKWCPTPDCGYIIELTDGCSNTS-----HVTCSKCGHEFCFNCKEEWHEGLTC 65
RING-HC_RBR_RNF14 cd16628
RING finger, HC subclass, found in RING finger protein 14 (RNF14) and similar proteins; RNF14, ...
154-205 2.44e-06

RING finger, HC subclass, found in RING finger protein 14 (RNF14) and similar proteins; RNF14, also known as androgen receptor-associated protein 54 (ARA54), HFB30, or Triad2 protein, is an RBR-type E3 ubiquitin-protein ligase that is highly expressed in the testis and interacts with class III E2s (UBE2E2, UbcH6, and UBE2E3). Its differential localization may play an important role in testicular development and spermatogenesis in humans. RNF14 functions as a transcriptional regulator of mitochondrial and immune function in muscle. It is a ligand-dependent androgen receptor (AR) co-activator and may also may participate in enhancing cell cycle progression and cell proliferation via induction of cyclin D1. Moreover, RNF14 is crucial for colon cancer cell survival. It acts as a new enhancer of the Wnt-dependent transcriptional outputs that acts at the level of the T-cell factor/lymphoid enhancer factor (TCF/LEF)-beta-catenin complex. RNF14 contains an N-terminal RWD domain and a C-terminal RBR domain. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination.


Pssm-ID: 438290  Cd Length: 59  Bit Score: 44.22  E-value: 2.44e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15229763 154 TCSICFNNVLeAEKMFSVAICGHQFCVECVKHYIEVKLLEGGVP--RCLDYQCE 205
Cdd:cd16628   7 TCNICFLDKL-GSECMYFKDCGHVYCKECLKEYFEVQIRDGNVTslNCPEPKCA 59
Rcat_RBR_unk cd22584
Rcat domain found in an uncharacterized subfamily of RBR proteins; This subfamily contains ...
316-339 5.09e-05

Rcat domain found in an uncharacterized subfamily of RBR proteins; This subfamily contains uncharacterized members of the RBR family, including Arabidopsis thaliana mutator-like transposase and hypothetical protein At2g19610/F3P11.21. The RBR family of RING-type E3 ligases are characterized by containing a RBR domain, which was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. It is composed of an extended RING domain (RING1) followed by an in-between RING (IBR) domain and the catalytic domain, which is structurally an IBR domain but is commonly designated RING2. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently, where the IBR and RING2 domains have been renamed as BRcat and Rcat domains, respectively. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. This model corresponds to the Rcat domain that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain.


Pssm-ID: 439035  Cd Length: 37  Bit Score: 39.90  E-value: 5.09e-05
                        10        20
                ....*....|....*....|....
gi 15229763 316 KWSQCAKCQHMIARIEGCNVIICR 339
Cdd:cd22584   1 GWRRCPQCGHMVELSEGCNHMTCR 24
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
30-86 1.27e-03

RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties.


Pssm-ID: 260011 [Multi-domain]  Cd Length: 128  Bit Score: 38.22  E-value: 1.27e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15229763  30 AGFGVAIFDqDDKLLFQMKRPIhGSDITVLEAELTALKQGLTETMKLGLDRISICCD 86
Cdd:cd09279  16 AGAGVVIYS-PGGEVLELSERL-GFPATNNEAEYEALIAGLELALELGAEKLEIYGD 70
 
Name Accession Description Interval E-value
BRcat_RBR_unk cd22582
BRcat domain found in an uncharacterized subfamily of RBR proteins; This subfamily contains ...
236-294 1.14e-24

BRcat domain found in an uncharacterized subfamily of RBR proteins; This subfamily contains uncharacterized members of the RBR family, including Arabidopsis thaliana mutator-like transposase, hypothetical protein F9K21.90, and hypothetical protein T16H5.30. The RBR family of RING-type E3 ligases are characterized by containing a RBR domain, which was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. It is composed of an extended RING domain (RING1) followed by an in-between RING (IBR) domain and the catalytic domain, which is structurally an IBR domain but is commonly designated RING2. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently, where the IBR and RING2 domains have been renamed as BRcat and Rcat domains, respectively. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. The BRcat domain adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes.


Pssm-ID: 439033  Cd Length: 56  Bit Score: 94.74  E-value: 1.14e-24
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15229763 236 VAERVYCPNPRCSGLMSKTELStstEEDVSTRTCCVKCGEPFCINCKVPWHSNLSCDDY 294
Cdd:cd22582   1 VSERVYCPNPDCSALMSKDELL---EAEDDTPRECPKCRRLFCARCKVPWHAGLSCAEY 56
RVT_3 pfam13456
Reverse transcriptase-like; This domain is found in plants and appears to be part of a ...
26-139 1.33e-16

Reverse transcriptase-like; This domain is found in plants and appears to be part of a retrotransposon.


Pssm-ID: 433223 [Multi-domain]  Cd Length: 123  Bit Score: 74.99  E-value: 1.33e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229763    26 SQLLAGFGVAIFDQDDKLLFQMKRPIHGSdITVLEAELTALKQGLTETMKLGLDRISICCDHDHIYELVMGRStPEQDNI 105
Cdd:pfam13456   9 DSGLAGAGVVIRDPNGNVLLAGQKKLGPG-ASVLEAEAQALIIGLQLAWKLGIRHLIVEGDSATVVQLINGRS-PKQSKL 86
                          90       100       110
                  ....*....|....*....|....*....|....
gi 15229763   106 AMLMNDVQRMRQQLRYSNPILVTRDQISFAYKLA 139
Cdd:pfam13456  87 ANLLDEIRKLLKRFESVSFEHIPREQNRVADTLA 120
IBR smart00647
In Between Ring fingers; the domains occurs between pairs og RING fingers
225-291 3.04e-16

In Between Ring fingers; the domains occurs between pairs og RING fingers


Pssm-ID: 214763 [Multi-domain]  Cd Length: 64  Bit Score: 72.06  E-value: 3.04e-16
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15229763    225 WKQRIEEELILV-AERVYCPNPRCSGLMSKTElststeEDVSTRTCCVKCGEPFCINCKVPWHSNLSC 291
Cdd:smart00647   3 YERLLLESYVESnPDLKWCPAPDCSAAIIVTE------EEGCNRVTCPKCGFSFCFRCKVPWHSPVSC 64
IBR pfam01485
IBR domain, a half RING-finger domain; The IBR (In Between Ring fingers) domain is often found ...
226-291 4.75e-09

IBR domain, a half RING-finger domain; The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (pfam00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain. Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organizms. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. The ubiquitin ligase Parkin is an RBR family protein whose mutations are involved in forms of familial Parkinson's disease.


Pssm-ID: 460227  Cd Length: 65  Bit Score: 52.16  E-value: 4.75e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15229763   226 KQRIEEELILVAERVYCPNPRCSGLMSKTELSTSTEedvstRTCCVKCGEPFCINCKVPWHSNLSC 291
Cdd:pfam01485   5 KLLLKSYVESDPNLKWCPTPDCGYIIELTDGCSNTS-----HVTCSKCGHEFCFNCKEEWHEGLTC 65
BRcat_RBR cd20335
BRcat (benign-catalytic) domain, part of the RBR (RING1-BRcat-Rcat) domain; The RBR family of ...
237-294 1.92e-08

BRcat (benign-catalytic) domain, part of the RBR (RING1-BRcat-Rcat) domain; The RBR family of RING-type E3 ligases are characterized by containing an RBR domain, which was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. It is composed of an extended RING domain (RING1) followed by an in-between RING (IBR) domain and the catalytic domain, which is structurally an IBR domain but is commonly designated as RING2. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently, where the IBR and RING2 domains have been renamed as BRcat and Rcat domains, respectively. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. The BRcat domain adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. The model corresponds to the BRcat domain.


Pssm-ID: 438996  Cd Length: 53  Bit Score: 50.23  E-value: 1.92e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15229763 237 AERVYCPNPRCSGLMSKTELSTSTeedvstRTCCVKCGEPFCINCKVPWHSNLSCDDY 294
Cdd:cd20335   2 PNLRWCPTPDCGGVIRVEEPGDGP------RVTCPSCGTSFCFKCKEEWHEGLTCEEY 53
BRcat_RBR_RNF144 cd20349
BRcat domain found in the RNF144 protein subfamily; The RNF144 subfamily includes RNF144A and ...
239-296 3.64e-07

BRcat domain found in the RNF144 protein subfamily; The RNF144 subfamily includes RNF144A and RNF144B, which are transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligases. RNF144A, also called UbcM4-interacting protein 4 (UIP4), or ubiquitin-conjugating enzyme 7-interacting protein 4, targets DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and thus promotes DNA damage-induced cell apoptosis. It is transcriptionally repressed by metastasis-associated protein 1 (MTA1) and inhibits MTA1-driven cancer cell migration and invasion. RNF144B, also called PIR2, IBR domain-containing protein 2 (IBRDC2), or p53-inducible RING finger protein (p53RFP), induces p53-dependent but caspase-independent apoptosis. It interacts with E2 ubiquitin-conjugating enzymes UbcH7 and UbcH8, but not with UbcH5. It is involved in ubiquitination and degradation of p21, a p53 downstream protein promoting growth arrest and antagonizing apoptosis, suggesting a role in switching a cell from p53-mediated growth arrest to apoptosis. Moreover, RNF144B regulates the levels of Bax, a pro-apoptotic protein from the Bcl-2 family, and protects cells from unprompted Bax activation and cell death. It also regulates epithelial homeostasis by mediating degradation of p21WAF1 and p63. Both RNF144A and RNF144B contain an RBR domain followed by a potential single-TM domain. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of the RNF144 protein subfamily that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity.


Pssm-ID: 439010  Cd Length: 64  Bit Score: 46.61  E-value: 3.64e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15229763 239 RVYCPNPRCSGLMSKTElSTSTEEDVSTRTCCVKCGEPFCINCKVPWHSNLSCDDYKR 296
Cdd:cd20349   8 RTWCPRAGCETVCHVCP-PSGSAPVTAVPVQCPKCGLTFCSICKAAWHAGQSCDENMK 64
RING-HC_RBR_RNF14 cd16628
RING finger, HC subclass, found in RING finger protein 14 (RNF14) and similar proteins; RNF14, ...
154-205 2.44e-06

RING finger, HC subclass, found in RING finger protein 14 (RNF14) and similar proteins; RNF14, also known as androgen receptor-associated protein 54 (ARA54), HFB30, or Triad2 protein, is an RBR-type E3 ubiquitin-protein ligase that is highly expressed in the testis and interacts with class III E2s (UBE2E2, UbcH6, and UBE2E3). Its differential localization may play an important role in testicular development and spermatogenesis in humans. RNF14 functions as a transcriptional regulator of mitochondrial and immune function in muscle. It is a ligand-dependent androgen receptor (AR) co-activator and may also may participate in enhancing cell cycle progression and cell proliferation via induction of cyclin D1. Moreover, RNF14 is crucial for colon cancer cell survival. It acts as a new enhancer of the Wnt-dependent transcriptional outputs that acts at the level of the T-cell factor/lymphoid enhancer factor (TCF/LEF)-beta-catenin complex. RNF14 contains an N-terminal RWD domain and a C-terminal RBR domain. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination.


Pssm-ID: 438290  Cd Length: 59  Bit Score: 44.22  E-value: 2.44e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15229763 154 TCSICFNNVLeAEKMFSVAICGHQFCVECVKHYIEVKLLEGGVP--RCLDYQCE 205
Cdd:cd16628   7 TCNICFLDKL-GSECMYFKDCGHVYCKECLKEYFEVQIRDGNVTslNCPEPKCA 59
RING-HC_RBR_TRIAD1 cd16773
RING finger, HC subclass, found in two RING fingers and DRIL [double RING finger linked] 1 ...
154-206 4.75e-06

RING finger, HC subclass, found in two RING fingers and DRIL [double RING finger linked] 1 (TRIAD1); TRIAD1, also known as ariadne-2 (ARI-2), protein ariadne-2 homolog, Ariadne RBR E3 ubiquitin protein ligase 2 (ARIH2), or UbcM4-interacting protein 48, is an RBR-type E3 ubiquitin-protein ligase that catalyzes the formation of polyubiquitin chains linked via lysine-48, as well as lysine-63 residues. Its auto-ubiquitylation can be catalyzed by the E2 conjugating enzyme UBCH7. TRIAD1 has been implicated in hematopoiesis, specifically in myelopoiesis, as well as in embryogenesis. It functions as a regulator of endosomal transport and is required for the proper function of multivesicular bodies. It also acts as a novel ubiquitination target for proteasome-dependent degradation by murine double minute 2 (MDM2). As a proapoptotic protein, TRIAD1 promotes p53 activation, and inhibits MDM2-mediated p53 ubiquitination and degradation. Furthermore, TRIAD1 can inhibit the ubiquitination and proteasomal degradation of growth factor independence 1 (Gfi1), a transcriptional repressor essential for the function and development of many different hematopoietic lineages. TRIAD1 contains an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination.


Pssm-ID: 438429 [Multi-domain]  Cd Length: 54  Bit Score: 43.50  E-value: 4.75e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 15229763 154 TCSICFNNVlEAEKMFSVAiCGHQFCVECVKHYIEVKLLEGGVP--RCLDYQCES 206
Cdd:cd16773   2 TCGVCCEDV-PKDELFSLA-CGHYFCNDCWKQYLTVKIKDGVSTgiECMAPDCKV 54
RING-HC_ARI6-like cd23141
RING finger, HC subclass, found in Arabidopsis thaliana protein ariadne homolog 6 (ARI6) and ...
154-214 7.17e-06

RING finger, HC subclass, found in Arabidopsis thaliana protein ariadne homolog 6 (ARI6) and similar proteins; This subfamily includes ARI6 and ARI11. They might act as E3 ubiquitin-protein ligases, or as part of E3 complexes, which accept ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfer it to substrates. Members of this subfamily contain a typical C3HC4-type RING-HC finger.


Pssm-ID: 438503 [Multi-domain]  Cd Length: 62  Bit Score: 43.24  E-value: 7.17e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15229763 154 TCSICFNNvLEAEKMFSVAiCGHQFCVECVKHYIEVKLLEGgvPRCLDYQCESkltlTSCG 214
Cdd:cd23141   3 TCGICFES-FPVEEMRAAS-CGHYFCKTCWTGYIHTAISDG--PGCLDLRCPD----PSCP 55
Rcat_RBR_unk cd22584
Rcat domain found in an uncharacterized subfamily of RBR proteins; This subfamily contains ...
316-339 5.09e-05

Rcat domain found in an uncharacterized subfamily of RBR proteins; This subfamily contains uncharacterized members of the RBR family, including Arabidopsis thaliana mutator-like transposase and hypothetical protein At2g19610/F3P11.21. The RBR family of RING-type E3 ligases are characterized by containing a RBR domain, which was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. It is composed of an extended RING domain (RING1) followed by an in-between RING (IBR) domain and the catalytic domain, which is structurally an IBR domain but is commonly designated RING2. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently, where the IBR and RING2 domains have been renamed as BRcat and Rcat domains, respectively. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. This model corresponds to the Rcat domain that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain.


Pssm-ID: 439035  Cd Length: 37  Bit Score: 39.90  E-value: 5.09e-05
                        10        20
                ....*....|....*....|....
gi 15229763 316 KWSQCAKCQHMIARIEGCNVIICR 339
Cdd:cd22584   1 GWRRCPQCGHMVELSEGCNHMTCR 24
BRcat_RBR_RNF14 cd20341
BRcat domain found in RING finger protein 14 (RNF14); RNF14, also called androgen receptor (AR) ...
240-292 1.25e-03

BRcat domain found in RING finger protein 14 (RNF14); RNF14, also called androgen receptor (AR)-associated protein 54 (ARA54), HFB30, or Triad2 protein, is an RBR-type E3 ubiquitin-protein ligase that is highly expressed in the testis and interacts with class III E2s (UBE2E2, UbcH6, and UBE2E3). Its differential localization may play an important role in testicular development and spermatogenesis in humans. RNF14 functions as a transcriptional regulator of mitochondrial and immune function in muscles. It is a ligand-dependent AR co-activator that enhances AR-dependent transcriptional activation. It may also participate in enhancing cell cycle progression and cell proliferation via induction of cyclin D1. Moreover, RNF14 is crucial for colon cancer cell survival. It acts as a new enhancer of the Wnt-dependent transcriptional outputs that acts at the level of the T-cell factor/lymphoid enhancer factor (TCF/LEF)-beta-catenin complex. RNF14 contains an N-terminal RWD domain, and a C-terminal RBR domain. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of RNF14 that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity.


Pssm-ID: 439002  Cd Length: 57  Bit Score: 36.51  E-value: 1.25e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 15229763 240 VYCPNPRCSGLmsktelstSTEEDVSTRTCCVKCGEPFCINCKVPWHSNLSCD 292
Cdd:cd20341   8 VYCPRPSCQTP--------VILEPDENLGICPSCNYAFCTLCRETYHGVSPCK 52
RNase_HI_like cd09279
RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease ...
30-86 1.27e-03

RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI; Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties.


Pssm-ID: 260011 [Multi-domain]  Cd Length: 128  Bit Score: 38.22  E-value: 1.27e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 15229763  30 AGFGVAIFDqDDKLLFQMKRPIhGSDITVLEAELTALKQGLTETMKLGLDRISICCD 86
Cdd:cd09279  16 AGAGVVIYS-PGGEVLELSERL-GFPATNNEAEYEALIAGLELALELGAEKLEIYGD 70
BRcat_RBR_RNF217 cd20342
BRcat domain found in RING finger protein 217 (RNF217); RNF217, also termed IBR ...
245-296 1.34e-03

BRcat domain found in RING finger protein 217 (RNF217); RNF217, also termed IBR domain-containing protein 1 (IBRDC1), is a transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligase mainly expressed in testis and skeletal muscle with different splice variants. It interacts with the anti-apoptotic protein HAX1, and is adjacent to a translocation breakpoint involving ETV6 in childhood acute lymphoblastic leukemia (ALL). RNF217 contains a RBR domain followed by TMs. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain use an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. The family corresponds to the BRcat (benign-catalytic) domain that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity.


Pssm-ID: 439003  Cd Length: 74  Bit Score: 36.96  E-value: 1.34e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 15229763 245 PRCSGLMS----KTELSTSTEEDVSTRtcCVKCGEPFCINCKVPWHSNLSCDDYKR 296
Cdd:cd20342  10 PRCSHVTTrpkkELIKKKKSEGGLKVQ--CPTCQLVWCFKCHAPWHEGITCKEYKK 63
RING-HC_RBR_HEL2-like cd16625
RING finger, HC subclass, found in Saccharomyces cerevisiae histone E3 ligase 2 (HEL2) and ...
154-204 1.53e-03

RING finger, HC subclass, found in Saccharomyces cerevisiae histone E3 ligase 2 (HEL2) and similar proteins; HEL2 is an E3 ubiquitin-protein ligase that interacts with the E2 ubiquitin-conjugating enzyme UBC4 and histones H3 and H4. It plays an important role in regulating histone protein levels and also likely to contribute to the maintenance of genomic stability in the budding yeast. HEL2 can be phosphorylated by the DNA damage checkpoint kinase and histone protein regulator Rad53. This subfamily also includes Schizosaccharomyces pombe histone E3 ligase 1 (HEL1), also known as DNA-break-localizing protein 4 (dbl4), and Dictyostelium discoideum Ariadne-like ubiquitin ligase (RbrA). RbrA may act as an E3 ubiquitin-protein ligase that appears to be required for normal cell-type proportioning and cell sorting during multicellular development, and is also necessary for spore cell viability. Members of this subfamily contain an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination.


Pssm-ID: 438287  Cd Length: 57  Bit Score: 36.20  E-value: 1.53e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 15229763 154 TCSICFNnvlEAEKMFSVAICGHQFCVECVKHYIEVKLLEGG---VPRCLDYQC 204
Cdd:cd16625   2 ECPICCD---DGELETFSLECGHEFCVDCYSQYLTSKIKEEGegcRITCPGEKC 52
RING-HC_RBR_HHARI cd16626
RING finger, HC subclass, found in human homolog of Drosophila ariadne (HHARI) and similar ...
155-195 2.18e-03

RING finger, HC subclass, found in human homolog of Drosophila ariadne (HHARI) and similar proteins; This subfamily includes Drosophila melanogaster protein ariadne-1 (ARI-1), and its eukaryotic homologs, such as HHARI. ARI-1 is a widely expressed Drosophila RING-finger protein that localizes mainly in the cytoplasm and is required for neural development. It interacts with a novel ubiquitin-conjugating enzyme, UbcD10. HHARI, also known as H7-AP2, monocyte protein 6 (MOP-6), protein ariadne-1 homolog, Ariadne RBR E3 ubiquitin protein ligase 1 (ARIH1), ariadne-1 (ARI-1), UbcH7-binding protein, UbcM4-interacting protein, or ubiquitin-conjugating enzyme E2-binding protein 1, is an RBR-type E3 ubiquitin-protein ligase highly expressed in nuclei, where it is co-localized with nuclear bodies including Cajal, PML, and Lewy bodies. It interacts with the E2 conjugating enzymes UbcH7, UbcH8, UbcM4, and UbcD10 in human, mouse, and fly, and modulates the ubiquitylation of substrate proteins including single-minded 2 (SIM2) and translation initiation factor 4E homologous protein (4EHP). It functions as a potent mediator of DNA damage-induced translation arrest, which protects stem and cancer cells against genotoxic stress by initiating a 4EHP-mediated mRNA translation arrest. HHARI contains an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination.


Pssm-ID: 438288  Cd Length: 59  Bit Score: 35.79  E-value: 2.18e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 15229763 155 CSICFNNvLEAEKMFSVAiCGHQFCVECVKHYIEVKLLEGG 195
Cdd:cd16626   3 CDICYLN-YPNSYMTGLE-CGHKFCMQCWKEYLTTKIMEEG 41
BRcat_RBR_HOIP cd20337
BRcat domain found in HOIL-1-interacting protein (HOIP) and similar proteins; HOIP, also ...
270-295 2.60e-03

BRcat domain found in HOIL-1-interacting protein (HOIP) and similar proteins; HOIP, also called RING finger protein 31 (RNF31) or zinc in-between-RING-finger ubiquitin-associated domain protein, together with HOIL-1 and SHARPIN, forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis. It also interacts with the atypical mammalian orphan receptor DAX-1, trigger DAX-1 ubiquitination and stabilization, and participate in repressing steroidogenic gene expression. HOIP contains three Npl4 zinc fingers, a central ubiquitin-associated (UBA) domain responsible for interaction with the N-terminal ubiquitin-like domain (UBL) of HOIL-1L, an RBR domain, and a C-terminal linear chain determining domain (LDD). The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of HOIP and similar proteins that adopt the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity.


Pssm-ID: 438998  Cd Length: 78  Bit Score: 36.09  E-value: 2.60e-03
                        10        20
                ....*....|....*....|....*....
gi 15229763 270 CVKCGEPFCINCKVPW---HSNLSCDDYK 295
Cdd:cd20337  43 CPQCGKVTCFKCKKPWedqHEGISCEQFQ 71
BRcat_RBR_parkin cd20340
BRcat domain found in parkin and similar proteins; Parkin, also called Parkinson juvenile ...
231-287 2.78e-03

BRcat domain found in parkin and similar proteins; Parkin, also called Parkinson juvenile disease protein 2, is an RBR-type E3 ubiquitin-protein ligase that is associated with recessive early onset Parkinson's disease (PD), and exerts a protective effect against dopamine-induced alpha-synuclein-dependent cell toxicity. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Parkin functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, RHOT1/MIRO1, MFN1, MFN2, STUB1, SNCAIP, SEPT5, TOMM20, USP30, ZNF746 and AIMP2. It mediates monoubiquitination as well as Lys6-, Lys11-, Lys48- and Lys63-linked polyubiquitination of substrates depending on the context. Parkin may enhance cell viability and protects dopaminergic neurons from oxidative stress-mediated death by regulating mitochondrial function. It also limits the production of reactive oxygen species (ROS), and regulates cyclin-E during neuronal apoptosis. Moreover, parkin displays a ubiquitin ligase-independent function in transcriptional repression of p53. Parkin contains an N-terminal ubiquitin-like domain and a C-terminal RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of parkin that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity.


Pssm-ID: 439001  Cd Length: 77  Bit Score: 36.10  E-value: 2.78e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 15229763 231 EELILVAERVYCPNPRC-SGLMsktelstsTEEDVSTRTCCVKCGEPFCINCKVPWHS 287
Cdd:cd20340  21 EECVLQMGGVLCPQPGCgAGLL--------PEDECNRVTCELGCGFVFCRECLEAYHE 70
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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