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Conserved domains on  [gi|1977119052|gb|KAG2458480|]
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HOIL1 protein, partial [Polypterus senegalus]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Sharpin_PH super family cl48311
Sharpin PH domain; This PH domain is found at the N-terminus of sharpin and is involved in ...
17-139 4.78e-45

Sharpin PH domain; This PH domain is found at the N-terminus of sharpin and is involved in dimerization.


The actual alignment was detected with superfamily member pfam16764:

Pssm-ID: 465263  Cd Length: 113  Bit Score: 156.47  E-value: 4.78e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1977119052  17 TGCSTVVMSVrvsvcHSGIRPLCLpGAGTGDDSLRLQLSMDLGKAGEFHLALRDTsgastGRSVSIVEYNLRDIHYEIKN 96
Cdd:pfam16764   1 PGCATVLMSV-----HAGVRPLCA-GPGAEAESLRLQLSMDPERPGRFRLALRGT-----GPSAVILEFPLRSVSYEVKS 69
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1977119052  97 SQTHELVVIGHPDERMTFNFRDEKEAQKWSTIITSTMREVQRV 139
Cdd:pfam16764  70 PSCHELQPPPPPPGRLSFHFLDEQEAQEWATVVRSSLREAHRG 112
BRcat_RBR_HOIL1 cd20345
BRcat domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins; ...
547-611 2.26e-41

BRcat domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins; HOIL-1 is also called RBCK1, HOIL-1L, RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, Hepatitis B virus X-associated protein 4, RING finger protein 54 (RNF54), ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28). Together with E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), it forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has 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 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 HOIL1 that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity.


:

Pssm-ID: 439006  Cd Length: 65  Bit Score: 144.38  E-value: 2.26e-41
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1977119052 547 AESRTENSYHCATPDCRGWCEYEDNVNEFTCPICKKCNCLTCKAIHEGMNCRQYQDDLRIRALND 611
Cdd:cd20345     1 AESRSPNSFHCKTPDCPGWCFYEDDVNEFLCPVCKHTNCLTCKAIHEGMNCKEYQDDLRLRANND 65
Ubl_HOIL1 cd01799
ubiquitin-like (Ubl) domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and ...
221-300 2.11e-40

ubiquitin-like (Ubl) domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins; HOIL-1, also termed RBCK1, or HOIL-1L, or RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, or Hepatitis B virus X-associated protein 4, or RING finger protein 54 (RNF54), or ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28), together with E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has a 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 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.


:

Pssm-ID: 340497  Cd Length: 81  Bit Score: 142.35  E-value: 2.11e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1977119052 221 QEISMKVGVED-ATSSCCVTVKVFSYMTIASLKQQVFRDYGFHPKVQRWVIGQCLCVDDRSLSSYGIRRDGDTAFLYLVS 299
Cdd:cd01799     1 TEISIKVYVEDkSSSSGPITLKVRPHTTIASLKRQIFLEYGFPPSVQRWIIGKRLATDDETLLSYGIKDSGDPAFLYLVS 80

                  .
gi 1977119052 300 A 300
Cdd:cd01799    81 A 81
mRING-HC-C3HC3D_RBR_HOIL1 cd16633
Modified RING finger, HC subclass (C3HC3D-type), found in heme-oxidized IRP2 ubiquitin ligase ...
459-514 2.77e-27

Modified RING finger, HC subclass (C3HC3D-type), found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins; HOIL-1, also known as RBCK1, HOIL-1L, RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, Hepatitis B virus X-associated protein 4, RING finger protein 54 (RNF54), ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28), together with E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), form the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta, but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to the RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has 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 modified C3HC3D-type RING-HC finger required for RBR-mediated ubiquitination.


:

Pssm-ID: 438295 [Multi-domain]  Cd Length: 56  Bit Score: 104.65  E-value: 2.77e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1977119052 459 LVANREAVECRICYLDLAPGEGVLLRECLHCFCRDCLRSVIKLSEDPEVSCPYRDD 514
Cdd:cd16633     1 LVPNQEPFECPICFDDVPPGEGVVLRECLHSFCRECLRGAIQNSEEAEVKCPFRDD 56
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
383-404 3.21e-04

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.


:

Pssm-ID: 197784 [Multi-domain]  Cd Length: 25  Bit Score: 38.07  E-value: 3.21e-04
                           10        20
                   ....*....|....*....|..
gi 1977119052  383 WACPTCTFINKPTRPGCEICCH 404
Cdd:smart00547   3 WECPACTFLNFASRSKCFACGA 24
 
Name Accession Description Interval E-value
Sharpin_PH pfam16764
Sharpin PH domain; This PH domain is found at the N-terminus of sharpin and is involved in ...
17-139 4.78e-45

Sharpin PH domain; This PH domain is found at the N-terminus of sharpin and is involved in dimerization.


Pssm-ID: 465263  Cd Length: 113  Bit Score: 156.47  E-value: 4.78e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1977119052  17 TGCSTVVMSVrvsvcHSGIRPLCLpGAGTGDDSLRLQLSMDLGKAGEFHLALRDTsgastGRSVSIVEYNLRDIHYEIKN 96
Cdd:pfam16764   1 PGCATVLMSV-----HAGVRPLCA-GPGAEAESLRLQLSMDPERPGRFRLALRGT-----GPSAVILEFPLRSVSYEVKS 69
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1977119052  97 SQTHELVVIGHPDERMTFNFRDEKEAQKWSTIITSTMREVQRV 139
Cdd:pfam16764  70 PSCHELQPPPPPPGRLSFHFLDEQEAQEWATVVRSSLREAHRG 112
BRcat_RBR_HOIL1 cd20345
BRcat domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins; ...
547-611 2.26e-41

BRcat domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins; HOIL-1 is also called RBCK1, HOIL-1L, RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, Hepatitis B virus X-associated protein 4, RING finger protein 54 (RNF54), ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28). Together with E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), it forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has 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 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 HOIL1 that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity.


Pssm-ID: 439006  Cd Length: 65  Bit Score: 144.38  E-value: 2.26e-41
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1977119052 547 AESRTENSYHCATPDCRGWCEYEDNVNEFTCPICKKCNCLTCKAIHEGMNCRQYQDDLRIRALND 611
Cdd:cd20345     1 AESRSPNSFHCKTPDCPGWCFYEDDVNEFLCPVCKHTNCLTCKAIHEGMNCKEYQDDLRLRANND 65
Ubl_HOIL1 cd01799
ubiquitin-like (Ubl) domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and ...
221-300 2.11e-40

ubiquitin-like (Ubl) domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins; HOIL-1, also termed RBCK1, or HOIL-1L, or RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, or Hepatitis B virus X-associated protein 4, or RING finger protein 54 (RNF54), or ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28), together with E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has a 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 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.


Pssm-ID: 340497  Cd Length: 81  Bit Score: 142.35  E-value: 2.11e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1977119052 221 QEISMKVGVED-ATSSCCVTVKVFSYMTIASLKQQVFRDYGFHPKVQRWVIGQCLCVDDRSLSSYGIRRDGDTAFLYLVS 299
Cdd:cd01799     1 TEISIKVYVEDkSSSSGPITLKVRPHTTIASLKRQIFLEYGFPPSVQRWIIGKRLATDDETLLSYGIKDSGDPAFLYLVS 80

                  .
gi 1977119052 300 A 300
Cdd:cd01799    81 A 81
PH_SHARPIN cd13305
SHANK-associated RH domain interacting protein Pleckstrin homology (PH) domain; SHARPIN has a ...
25-139 1.34e-35

SHANK-associated RH domain interacting protein Pleckstrin homology (PH) domain; SHARPIN has a variety of roles including: a role as a scaffolding partner of anchoring/scaffold proteins Shank1, a role in carcinogenesis through the interaction with FYN binding protein (FYB), which binds to oncogene FYN, a role in apoptosis by interacting with AIFM1, a mitochondrial regulator of cell death, CAPN13, and NSD1, as well as a role in immune disease and inflammation. SHARPIN has at its N-terminus a PH domain, followed by a E3 ubiquitin ligase domain, and a C-terminal RanBP-type and C3HC4-type zinc finger containing 1 domain (RBCK1, also known as HOIP which functions as a protein kinase C (PKC) binding protein as well as a transcriptional activator. SHARPIN's PH domain functions as a dimerization module, rather than a ligand recognition domain. Instead it acts as a dimerization module extending the functional applications of this superfold. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.


Pssm-ID: 270115  Cd Length: 114  Bit Score: 130.01  E-value: 1.34e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1977119052  25 SVRVSVCHSGIRPLCLPGAGTGDDSLRLQLSMDLGKAGEFHLALRDTSGAstGRSVSIVEYNLRDIHYEIKNSQTHELVV 104
Cdd:cd13305     1 AVEEAVVHSEVRPLGPGSPPAPDGLLRLQLSADPARPGRFRLALQGAGDS--GPPGEGLEWPLKSVSYEVKTPTCHELQP 78
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1977119052 105 IGHPDERMTFNFRDEKEAQKWSTIITSTMREVQRV 139
Cdd:cd13305    79 PKPPPDALSFHFQDEQEAQRWATVVERALREAQRG 113
mRING-HC-C3HC3D_RBR_HOIL1 cd16633
Modified RING finger, HC subclass (C3HC3D-type), found in heme-oxidized IRP2 ubiquitin ligase ...
459-514 2.77e-27

Modified RING finger, HC subclass (C3HC3D-type), found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins; HOIL-1, also known as RBCK1, HOIL-1L, RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, Hepatitis B virus X-associated protein 4, RING finger protein 54 (RNF54), ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28), together with E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), form the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta, but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to the RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has 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 modified C3HC3D-type RING-HC finger required for RBR-mediated ubiquitination.


Pssm-ID: 438295 [Multi-domain]  Cd Length: 56  Bit Score: 104.65  E-value: 2.77e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1977119052 459 LVANREAVECRICYLDLAPGEGVLLRECLHCFCRDCLRSVIKLSEDPEVSCPYRDD 514
Cdd:cd16633     1 LVPNQEPFECPICFDDVPPGEGVVLRECLHSFCRECLRGAIQNSEEAEVKCPFRDD 56
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
383-404 3.21e-04

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.


Pssm-ID: 197784 [Multi-domain]  Cd Length: 25  Bit Score: 38.07  E-value: 3.21e-04
                           10        20
                   ....*....|....*....|..
gi 1977119052  383 WACPTCTFINKPTRPGCEICCH 404
Cdd:smart00547   3 WECPACTFLNFASRSKCFACGA 24
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
235-298 4.54e-04

Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression


Pssm-ID: 214563 [Multi-domain]  Cd Length: 72  Bit Score: 39.16  E-value: 4.54e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1977119052  235 SCCVTVKVFSYMTIASLKQQVFRDYGFHPKVQRwVI--GQCLcVDDRSLSSYGIrrdGDTAFLYLV 298
Cdd:smart00213  10 GKTITLEVKPSDTVSELKEKIAELTGIPPEQQR-LIykGKVL-EDDRTLADYGI---QDGSTIHLV 70
IBR pfam01485
IBR domain, a half RING-finger domain; The IBR (In Between Ring fingers) domain is often found ...
556-597 7.79e-04

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: 38.30  E-value: 7.79e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1977119052 556 HCATPDCRGWCEYED---NVNEFTCPICKKCNCLTCKAI-HEGMNC 597
Cdd:pfam01485  20 WCPTPDCGYIIELTDgcsNTSHVTCSKCGHEFCFNCKEEwHEGLTC 65
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
238-297 1.89e-03

Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.


Pssm-ID: 459726 [Multi-domain]  Cd Length: 72  Bit Score: 37.54  E-value: 1.89e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1977119052 238 VTVKVFSYMTIASLKQQVFRDYGFHPKVQRWVI-GQCLcVDDRSLSSYGIrRDGDTAFLYL 297
Cdd:pfam00240  11 ITLEVDPTDTVLELKEKIAEKEGVPPEQQRLIYsGKVL-EDDQTLGEYGI-EDGSTIHLVL 69
 
Name Accession Description Interval E-value
Sharpin_PH pfam16764
Sharpin PH domain; This PH domain is found at the N-terminus of sharpin and is involved in ...
17-139 4.78e-45

Sharpin PH domain; This PH domain is found at the N-terminus of sharpin and is involved in dimerization.


Pssm-ID: 465263  Cd Length: 113  Bit Score: 156.47  E-value: 4.78e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1977119052  17 TGCSTVVMSVrvsvcHSGIRPLCLpGAGTGDDSLRLQLSMDLGKAGEFHLALRDTsgastGRSVSIVEYNLRDIHYEIKN 96
Cdd:pfam16764   1 PGCATVLMSV-----HAGVRPLCA-GPGAEAESLRLQLSMDPERPGRFRLALRGT-----GPSAVILEFPLRSVSYEVKS 69
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1977119052  97 SQTHELVVIGHPDERMTFNFRDEKEAQKWSTIITSTMREVQRV 139
Cdd:pfam16764  70 PSCHELQPPPPPPGRLSFHFLDEQEAQEWATVVRSSLREAHRG 112
BRcat_RBR_HOIL1 cd20345
BRcat domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins; ...
547-611 2.26e-41

BRcat domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins; HOIL-1 is also called RBCK1, HOIL-1L, RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, Hepatitis B virus X-associated protein 4, RING finger protein 54 (RNF54), ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28). Together with E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), it forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has 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 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 HOIL1 that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity.


Pssm-ID: 439006  Cd Length: 65  Bit Score: 144.38  E-value: 2.26e-41
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1977119052 547 AESRTENSYHCATPDCRGWCEYEDNVNEFTCPICKKCNCLTCKAIHEGMNCRQYQDDLRIRALND 611
Cdd:cd20345     1 AESRSPNSFHCKTPDCPGWCFYEDDVNEFLCPVCKHTNCLTCKAIHEGMNCKEYQDDLRLRANND 65
Ubl_HOIL1 cd01799
ubiquitin-like (Ubl) domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and ...
221-300 2.11e-40

ubiquitin-like (Ubl) domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins; HOIL-1, also termed RBCK1, or HOIL-1L, or RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, or Hepatitis B virus X-associated protein 4, or RING finger protein 54 (RNF54), or ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28), together with E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has a 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 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.


Pssm-ID: 340497  Cd Length: 81  Bit Score: 142.35  E-value: 2.11e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1977119052 221 QEISMKVGVED-ATSSCCVTVKVFSYMTIASLKQQVFRDYGFHPKVQRWVIGQCLCVDDRSLSSYGIRRDGDTAFLYLVS 299
Cdd:cd01799     1 TEISIKVYVEDkSSSSGPITLKVRPHTTIASLKRQIFLEYGFPPSVQRWIIGKRLATDDETLLSYGIKDSGDPAFLYLVS 80

                  .
gi 1977119052 300 A 300
Cdd:cd01799    81 A 81
PH_SHARPIN cd13305
SHANK-associated RH domain interacting protein Pleckstrin homology (PH) domain; SHARPIN has a ...
25-139 1.34e-35

SHANK-associated RH domain interacting protein Pleckstrin homology (PH) domain; SHARPIN has a variety of roles including: a role as a scaffolding partner of anchoring/scaffold proteins Shank1, a role in carcinogenesis through the interaction with FYN binding protein (FYB), which binds to oncogene FYN, a role in apoptosis by interacting with AIFM1, a mitochondrial regulator of cell death, CAPN13, and NSD1, as well as a role in immune disease and inflammation. SHARPIN has at its N-terminus a PH domain, followed by a E3 ubiquitin ligase domain, and a C-terminal RanBP-type and C3HC4-type zinc finger containing 1 domain (RBCK1, also known as HOIP which functions as a protein kinase C (PKC) binding protein as well as a transcriptional activator. SHARPIN's PH domain functions as a dimerization module, rather than a ligand recognition domain. Instead it acts as a dimerization module extending the functional applications of this superfold. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.


Pssm-ID: 270115  Cd Length: 114  Bit Score: 130.01  E-value: 1.34e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1977119052  25 SVRVSVCHSGIRPLCLPGAGTGDDSLRLQLSMDLGKAGEFHLALRDTSGAstGRSVSIVEYNLRDIHYEIKNSQTHELVV 104
Cdd:cd13305     1 AVEEAVVHSEVRPLGPGSPPAPDGLLRLQLSADPARPGRFRLALQGAGDS--GPPGEGLEWPLKSVSYEVKTPTCHELQP 78
                          90       100       110
                  ....*....|....*....|....*....|....*
gi 1977119052 105 IGHPDERMTFNFRDEKEAQKWSTIITSTMREVQRV 139
Cdd:cd13305    79 PKPPPDALSFHFQDEQEAQRWATVVERALREAQRG 113
mRING-HC-C3HC3D_RBR_HOIL1 cd16633
Modified RING finger, HC subclass (C3HC3D-type), found in heme-oxidized IRP2 ubiquitin ligase ...
459-514 2.77e-27

Modified RING finger, HC subclass (C3HC3D-type), found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins; HOIL-1, also known as RBCK1, HOIL-1L, RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, Hepatitis B virus X-associated protein 4, RING finger protein 54 (RNF54), ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28), together with E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), form the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta, but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to the RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has 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 modified C3HC3D-type RING-HC finger required for RBR-mediated ubiquitination.


Pssm-ID: 438295 [Multi-domain]  Cd Length: 56  Bit Score: 104.65  E-value: 2.77e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1977119052 459 LVANREAVECRICYLDLAPGEGVLLRECLHCFCRDCLRSVIKLSEDPEVSCPYRDD 514
Cdd:cd16633     1 LVPNQEPFECPICFDDVPPGEGVVLRECLHSFCRECLRGAIQNSEEAEVKCPFRDD 56
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
239-296 2.99e-08

ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like (Ubl) proteins have a similar ubiquitin (Ub) beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ub and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some Ubl domains have adaptor roles in Ub-signaling by mediating protein-protein interaction. Prokaryotic sulfur carrier proteins are Ub-related proteins that can be activated in an ATP-dependent manner. Polyubiquitination signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. One of these seven lysine residues (K27, Ub numbering) is conserved in this Ubl_ubiquitin_like family. K27-linked Ub chains are versatile and can be recognized by several downstream receptor proteins. K27 has roles beyond chain linkage, such as in Ubl NEDD8 (which contains many of the same lysines (K6, K11, K27, K33, K48) as Ub) where K27 has a role (other than conjugation) in the mechanism of protein neddylation.


Pssm-ID: 340559 [Multi-domain]  Cd Length: 68  Bit Score: 50.67  E-value: 2.99e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1977119052 239 TVKVFSYMTIASLKQQVFRDYGFHPKVQRWVIGQCLCVDDRSLSSYGIrRDGDTAFLY 296
Cdd:cd17039    12 TVEVDPDDTVADLKEKIEEKTGIPVEQQRLIYNGKELKDDKTLSDYGI-KDGSTIHLV 68
BRcat_RBR cd20335
BRcat (benign-catalytic) domain, part of the RBR (RING1-BRcat-Rcat) domain; The RBR family of ...
556-600 2.38e-07

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: 47.92  E-value: 2.38e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1977119052 556 HCATPDCRGWCEYEDNV--NEFTCPICKKCNCLTCKAI-HEGMNCRQY 600
Cdd:cd20335     6 WCPTPDCGGVIRVEEPGdgPRVTCPSCGTSFCFKCKEEwHEGLTCEEY 53
RING-HC_RAD5 cd23131
RING finger, HC subclass, found in radiation sensitivity protein 5 (RAD5) and similar proteins; ...
466-511 2.86e-04

RING finger, HC subclass, found in radiation sensitivity protein 5 (RAD5) and similar proteins; RAD5, also known as revertibility protein 2 (REV2), or DNA repair protein RAD5, is a probable helicase, and a member of the UBC2/RAD6 epistasis group. It functions with the DNA repair protein RAD18 in error-free postreplication DNA repair. It is involved in the maintenance of wild-type rates of instability of simple repetitive sequences such as poly(GT) repeats. It may also be involved in maintaining a balance which acts in favor of error-prone non-homologous joining during DNA double-strand breaks repairs. It recruits the UBC13-MMS2 dimer to chromatin for DNA repair. RAD5 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438493 [Multi-domain]  Cd Length: 65  Bit Score: 39.35  E-value: 2.86e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1977119052 466 VECRICYLDLAPGEGVLLRECLHCFCRDCLRSVIKLSEDPEVS--CPY 511
Cdd:cd23131     4 VECSICTQEPIEVGEVVFTECGHSFCEDCLLEYIEFQNKKKLDlkCPN 51
ZnF_RBZ smart00547
Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. ...
383-404 3.21e-04

Zinc finger domain; Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.


Pssm-ID: 197784 [Multi-domain]  Cd Length: 25  Bit Score: 38.07  E-value: 3.21e-04
                           10        20
                   ....*....|....*....|..
gi 1977119052  383 WACPTCTFINKPTRPGCEICCH 404
Cdd:smart00547   3 WECPACTFLNFASRSKCFACGA 24
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
235-298 4.54e-04

Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression


Pssm-ID: 214563 [Multi-domain]  Cd Length: 72  Bit Score: 39.16  E-value: 4.54e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1977119052  235 SCCVTVKVFSYMTIASLKQQVFRDYGFHPKVQRwVI--GQCLcVDDRSLSSYGIrrdGDTAFLYLV 298
Cdd:smart00213  10 GKTITLEVKPSDTVSELKEKIAELTGIPPEQQR-LIykGKVL-EDDRTLADYGI---QDGSTIHLV 70
IBR pfam01485
IBR domain, a half RING-finger domain; The IBR (In Between Ring fingers) domain is often found ...
556-597 7.79e-04

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: 38.30  E-value: 7.79e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1977119052 556 HCATPDCRGWCEYED---NVNEFTCPICKKCNCLTCKAI-HEGMNC 597
Cdd:pfam01485  20 WCPTPDCGYIIELTDgcsNTSHVTCSKCGHEFCFNCKEEwHEGLTC 65
BRcat_RBR_HOIP cd20337
BRcat domain found in HOIL-1-interacting protein (HOIP) and similar proteins; HOIP, also ...
565-601 1.20e-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: 38.01  E-value: 1.20e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1977119052 565 WC-------EYEDNVNEFTCPICKKCNCLTCK----AIHEGMNCRQYQ 601
Cdd:cd20337    24 WCahcsfgfIYEPEQLKMQCPQCGKVTCFKCKkpweDQHEGISCEQFQ 71
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
238-297 1.89e-03

Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.


Pssm-ID: 459726 [Multi-domain]  Cd Length: 72  Bit Score: 37.54  E-value: 1.89e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1977119052 238 VTVKVFSYMTIASLKQQVFRDYGFHPKVQRWVI-GQCLcVDDRSLSSYGIrRDGDTAFLYL 297
Cdd:pfam00240  11 ITLEVDPTDTVLELKEKIAEKEGVPPEQQRLIYsGKVL-EDDQTLGEYGI-EDGSTIHLVL 69
RING-HC_RBR_RNF19 cd16629
RING finger, HC subclass, found in the family of RING finger proteins RNF19A, RNF19B and ...
466-510 3.22e-03

RING finger, HC subclass, found in the family of RING finger proteins RNF19A, RNF19B and similar proteins; The family includes RING finger protein RNF19A and RNF19B, both of which are transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligases. RNF19A, also known as double ring-finger protein (Dorfin) or p38, localizes to the ubiquitylated inclusions in Parkinson's disease (PD), dementia with Lewy bodies, multiple system atrophy, and amyotrophic lateral sclerosis (ALS). It interacts with Psmc3, a protein component of the 19S regulatory cap of the 26S proteasome, and further participates in the ubiquitin-proteasome system in acrosome biogenesis, spermatid head shaping, and development of the head-tail coupling apparatus and tail. It modulates the ubiquitination and degradation of calcium-sensing receptor (CaR), which may contribute to a general mechanism for CaR quality control during biosynthesis. Moreover, RNF19A can also ubiquitylate mutant superoxide dismutase 1 (SOD1), the causative gene of familial ALS. It may associate with endoplasmic reticulum-associated degradation (ERAD) pathway, which is related to the pathogenesis of neurodegenerative disorders, such as PD or Alzheimer's disease. RNF19B, also known as IBR domain-containing protein 3 or natural killer lytic-associated molecule (NKLAM), plays a role in controlling tumor dissemination and metastasis. It is involved in the cytolytic function of natural killer (NK) cells and cytotoxic T lymphocytes (CTLs). It interacts with ubiquitin conjugates UbcH7 and UbcH8, and ubiquitinates uridine kinase like-1 (URKL-1) protein, targeting it for degradation. Moreover, RNF19B is a novel component of macrophage phagosomes and plays a role in macrophage anti-bacterial activity. It functions as a novel modulator of macrophage inducible nitric oxide synthase (iNOS) expression. Both RNF19A and RNF19B contain an RBR domain followed by three 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 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: 438291 [Multi-domain]  Cd Length: 56  Bit Score: 36.27  E-value: 3.22e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1977119052 466 VECRICYLDLAPGEGVLLRECLHCFCRDCLRSVIKLSEDPE---VSCP 510
Cdd:cd16629     1 LECPLCLDDLSPEFFPILLSCEHRSCRDCLRQYLTIEISESrvnISCP 48
Ubl2_FAT10 cd17053
ubiquitin-like (Ubl) domain 2 found in leukocyte antigen F (HLA-F) adjacent transcript 10 ...
239-295 8.27e-03

ubiquitin-like (Ubl) domain 2 found in leukocyte antigen F (HLA-F) adjacent transcript 10 (FAT10) and similar proteins; FAT10, also termed ubiquitin D (UBD), or diubiquitin, is a cytokine-inducible ubiquitin-like (Ubl) modifer that is highly expressed in the thymus, and targets substrates covalently for 26S proteasomal degradation. It is also associated with cancer development, antigen processing and antimicrobial defense, chromosomal stability and cell cycle regulation. FAT10 is presented on immune cells and under the inflammatory conditions, is synergistically induced by interferon gamma (IFNgamma) and tumor necrosis factor (TNFalpha) in the non-immune (liver parenchymal) cells. FAT10 contains two Ubl domains. The family corresponds to the second Ubl domain of FAT10. Some family members contain only one Ubl domain.


Pssm-ID: 340573  Cd Length: 71  Bit Score: 35.40  E-value: 8.27e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1977119052 239 TVKVFSYMTIASLKQQVFRDYGFHPKVQRWVI-GQCLCVDDRSLSSYGIRRdGDTAFL 295
Cdd:cd17053    14 TLQVSRSTTVAQVKAMIEDQSGVPPNEQILVYnGKRLEDGDKTLGEYGIKT-GDTLYL 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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