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Conserved domains on  [gi|392900600|ref|NP_001255513|]
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SP-RING-type domain-containing protein [Caenorhabditis elegans]

Protein Classification

RING finger protein( domain architecture ID 106764)

RING finger protein may function as an E3 ubiquitin protein ligase that mediates the ubiquitination of target proteins by bringing the ubiquitin-charged E2 ubiquitin-conjugating enzyme and the acceptor protein together to enable the direct transfer of ubiquitin

EC:  2.3.2.27
Gene Ontology:  GO:0061630

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PABP-1234 super family cl31127
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 31-155 2.90e-06

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


The actual alignment was detected with superfamily member TIGR01628:

Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 50.19  E-value: 2.90e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392900600   31 QMNGPPQHPGMQYSGQMQQLPYGQMeGNHAMYdqrimGQRAAGRPGMMP-DYPQMPMGQTPGNTMMRMPVQ--YPSGPSQ 107
Cdd:TIGR01628 379 QPRMRQLPMGSPMGGAMGQPPYYGQ-GPQQQF-----NGQPLGWPRMSMmPTPMGPGGPLRPNGLAPMNAVraPSRNAQN 452

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 392900600  108 MAGHPHMQQMQYghmmrappvsvygqMNNAQQYAVTaHPNPVPQPYYH 155
Cdd:TIGR01628 453 AAQKPPMQPVMY--------------PPNYQSLPLS-QDLPQPQSTAS 485
RING_Ubox super family cl17238
RING finger (Really Interesting New Gene) domain and U-box domain superfamily; The RING finger ...
 320-364 3.22e-03

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 cd16650:

Pssm-ID: 473075  Cd Length: 48  Bit Score: 35.71  E-value: 3.22e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 392900600 320 SLNCVLSKKRMFTPAKHHECKKI--FDLAQLINANKGMTRYFCQTCN 364
Cdd:cd16650    1 SLRCPLSLKRIKTPARGKHCKHLqcFDLDSYLEFNKRKPTWKCPICD 47
 
Name Accession Description Interval E-value
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 31-155 2.90e-06

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 50.19  E-value: 2.90e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392900600   31 QMNGPPQHPGMQYSGQMQQLPYGQMeGNHAMYdqrimGQRAAGRPGMMP-DYPQMPMGQTPGNTMMRMPVQ--YPSGPSQ 107
Cdd:TIGR01628 379 QPRMRQLPMGSPMGGAMGQPPYYGQ-GPQQQF-----NGQPLGWPRMSMmPTPMGPGGPLRPNGLAPMNAVraPSRNAQN 452

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 392900600  108 MAGHPHMQQMQYghmmrappvsvygqMNNAQQYAVTaHPNPVPQPYYH 155
Cdd:TIGR01628 453 AAQKPPMQPVMY--------------PPNYQSLPLS-QDLPQPQSTAS 485
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 17-147 1.86e-05

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 47.70  E-value: 1.86e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392900600   17 GHMPLGAGAASfPGQMNGPPQHPGMQYSGQMQQLPYGQMEGNHAMYDQRIMGQrAAGRPGMMPDYPQMPMGQTPGNTMMR 96
Cdd:pfam09606 100 GPMGPGPGGPM-GQQMGGPGTASNLLASLGRPQMPMGGAGFPSQMSRVGRMQP-GGQAGGMMQPSSGQPGSGTPNQMGPN 177

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 392900600   97 M-PVQYPS-GPSQMAGHPHMQQM--QYGHMMRAPPVSVYGQMNNAQQYAVTAHPN 147
Cdd:pfam09606 178 GgPGQGQAgGMNGGQQGPMGGQMppQMGVPGMPGPADAGAQMGQQAQANGGMNPQ 232
SP-RING_PIAS-like cd16650
SP-RING finger found in the Siz/PIAS RING (SP-RING) family of SUMO E3 ligases; The SP-RING ...
 320-364 3.22e-03

SP-RING finger found in the Siz/PIAS RING (SP-RING) family of SUMO E3 ligases; The SP-RING family includes PIAS (protein inhibitor of activated STAT) proteins, Zmiz proteins, and Siz proteins from plants and fungi. PIAS proteins modulate the activity of several transcription factors and act as E3 ubiquitin ligases in the sumoylation pathway. There are four members: PIAS1, PIAS2 (also known as PIASx), PIAS3, and PIAS4 (also known as PIASy). PIAS proteins were initially identified as inhibitors of activated STAT only, but are now known to interact with and modulate several other proteins, including androgen receptor (AR), tumor suppressor p53, and the transforming growth factor-beta (TGF-beta) signaling protein SMAD. They interact with STATs in a cytokine-dependent manner. PIAS proteins have SUMO E3-ligase activity and interaction of PIAS proteins with transcription factors often results in sumoylation of that protein. Zmiz1 (Zimp10) and its homolog Zmiz2 (Zimp7) were initially identified in humans as androgen receptor (AR) interacting proteins that function as transcriptional co-activators. They interact with BRG1, the catalytic subunit of the SWI-SNF remodeling complex. They also associate with other hormone nuclear receptors and transcription factors such as p53 and Smad3/Smad4, and regulate transcription of specific target genes by altering their chromatin structure. SIZ1 proteins from plants and fungi are also founding members of this family. SIZ1-mediated conjugation of SUMO1 and SUMO2 to other intracellular proteins is essential in Arabidopsis. Yeast SIZ proteins are SUMO E3 ligases involved in a novel pathway of chromosome maintenance. They enhance SUMO modification to many substrates in vivo, but also exhibit unique substrate specificity. PIAS proteins contain a specific RING finger known as Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription) RING (SP-RING) finger, which is essential for SUMO ligase activity. The SP-RING finger is a variant of the RING finger, which lacks the second, fifth, and sixth zinc-binding residues of the consensus C3H2C3-/C3HC4-type RING fingers. It binds a single Zn ion, instead of two ions bound by typical RING fingers.


Pssm-ID: 438312  Cd Length: 48  Bit Score: 35.71  E-value: 3.22e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 392900600 320 SLNCVLSKKRMFTPAKHHECKKI--FDLAQLINANKGMTRYFCQTCN 364
Cdd:cd16650    1 SLRCPLSLKRIKTPARGKHCKHLqcFDLDSYLEFNKRKPTWKCPICD 47
 
Name Accession Description Interval E-value
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 31-155 2.90e-06

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 50.19  E-value: 2.90e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392900600   31 QMNGPPQHPGMQYSGQMQQLPYGQMeGNHAMYdqrimGQRAAGRPGMMP-DYPQMPMGQTPGNTMMRMPVQ--YPSGPSQ 107
Cdd:TIGR01628 379 QPRMRQLPMGSPMGGAMGQPPYYGQ-GPQQQF-----NGQPLGWPRMSMmPTPMGPGGPLRPNGLAPMNAVraPSRNAQN 452

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 392900600  108 MAGHPHMQQMQYghmmrappvsvygqMNNAQQYAVTaHPNPVPQPYYH 155
Cdd:TIGR01628 453 AAQKPPMQPVMY--------------PPNYQSLPLS-QDLPQPQSTAS 485
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 17-147 1.86e-05

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 47.70  E-value: 1.86e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392900600   17 GHMPLGAGAASfPGQMNGPPQHPGMQYSGQMQQLPYGQMEGNHAMYDQRIMGQrAAGRPGMMPDYPQMPMGQTPGNTMMR 96
Cdd:pfam09606 100 GPMGPGPGGPM-GQQMGGPGTASNLLASLGRPQMPMGGAGFPSQMSRVGRMQP-GGQAGGMMQPSSGQPGSGTPNQMGPN 177

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 392900600   97 M-PVQYPS-GPSQMAGHPHMQQM--QYGHMMRAPPVSVYGQMNNAQQYAVTAHPN 147
Cdd:pfam09606 178 GgPGQGQAgGMNGGQQGPMGGQMppQMGVPGMPGPADAGAQMGQQAQANGGMNPQ 232
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 53-161 2.67e-04

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 44.03  E-value: 2.67e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392900600   53 GQMEGNHAMY-------DQRIM---GQRAAGRPGMmpdyPQMPMGQTPGNTMMRMPVQYPSGPSQMAG----HPHMQQMQ 118
Cdd:TIGR01628 348 GRMLGGKPLYvalaqrkEQRRAhlqDQFMQLQPRM----RQLPMGSPMGGAMGQPPYYGQGPQQQFNGqplgWPRMSMMP 423

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 392900600  119 YGHMMR--------APPVSVYGQMNNAQQYAVTAHPNPV---PQPYYHPEVRQL 161
Cdd:TIGR01628 424 TPMGPGgplrpnglAPMNAVRAPSRNAQNAAQKPPMQPVmypPNYQSLPLSQDL 477
Med15 pfam09606
ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of ...
 1-139 1.08e-03

ARC105 or Med15 subunit of Mediator complex non-fungal; The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development.


Pssm-ID: 312941 [Multi-domain]  Cd Length: 732  Bit Score: 42.30  E-value: 1.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392900600    1 MWPPQ-GVP-MSTPGSSAGHMPLGAGAAsfpGQMNGPPQHPGMQYSGQMQQLPYGQMEGNHAMYDQRIMGQRAAGRPGM- 77
Cdd:pfam09606 199 QMPPQmGVPgMPGPADAGAQMGQQAQAN---GGMNPQQMGGAPNQVAMQQQQPQQQGQQSQLGMGINQMQQMPQGVGGGa 275

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 392900600   78 ---MPDYPQMPMGQTPGNTMMRMPVQYPSGPSQMAGHPHMQQMQyGHMMRAPPVSVYGQMNNAQQ 139
Cdd:pfam09606 276 gqgGPGQPMGPPGQQPGAMPNVMSIGDQNNYQQQQTRQQQQQQG-GNHPAAHQQQMNQSVGQGGQ 339
SP-RING_PIAS-like cd16650
SP-RING finger found in the Siz/PIAS RING (SP-RING) family of SUMO E3 ligases; The SP-RING ...
 320-364 3.22e-03

SP-RING finger found in the Siz/PIAS RING (SP-RING) family of SUMO E3 ligases; The SP-RING family includes PIAS (protein inhibitor of activated STAT) proteins, Zmiz proteins, and Siz proteins from plants and fungi. PIAS proteins modulate the activity of several transcription factors and act as E3 ubiquitin ligases in the sumoylation pathway. There are four members: PIAS1, PIAS2 (also known as PIASx), PIAS3, and PIAS4 (also known as PIASy). PIAS proteins were initially identified as inhibitors of activated STAT only, but are now known to interact with and modulate several other proteins, including androgen receptor (AR), tumor suppressor p53, and the transforming growth factor-beta (TGF-beta) signaling protein SMAD. They interact with STATs in a cytokine-dependent manner. PIAS proteins have SUMO E3-ligase activity and interaction of PIAS proteins with transcription factors often results in sumoylation of that protein. Zmiz1 (Zimp10) and its homolog Zmiz2 (Zimp7) were initially identified in humans as androgen receptor (AR) interacting proteins that function as transcriptional co-activators. They interact with BRG1, the catalytic subunit of the SWI-SNF remodeling complex. They also associate with other hormone nuclear receptors and transcription factors such as p53 and Smad3/Smad4, and regulate transcription of specific target genes by altering their chromatin structure. SIZ1 proteins from plants and fungi are also founding members of this family. SIZ1-mediated conjugation of SUMO1 and SUMO2 to other intracellular proteins is essential in Arabidopsis. Yeast SIZ proteins are SUMO E3 ligases involved in a novel pathway of chromosome maintenance. They enhance SUMO modification to many substrates in vivo, but also exhibit unique substrate specificity. PIAS proteins contain a specific RING finger known as Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription) RING (SP-RING) finger, which is essential for SUMO ligase activity. The SP-RING finger is a variant of the RING finger, which lacks the second, fifth, and sixth zinc-binding residues of the consensus C3H2C3-/C3HC4-type RING fingers. It binds a single Zn ion, instead of two ions bound by typical RING fingers.


Pssm-ID: 438312  Cd Length: 48  Bit Score: 35.71  E-value: 3.22e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 392900600 320 SLNCVLSKKRMFTPAKHHECKKI--FDLAQLINANKGMTRYFCQTCN 364
Cdd:cd16650    1 SLRCPLSLKRIKTPARGKHCKHLqcFDLDSYLEFNKRKPTWKCPICD 47
 
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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