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Conserved domains on  [gi|1845970703|ref|NP_001370064|]
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Zip homologous protein 2 [Caenorhabditis elegans]

Protein Classification

RING finger protein( domain architecture ID 10630178)

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; similar to Homo sapiens E3 ubiquitin-protein ligase RNF10

CATH:  3.30.40.10
EC:  2.3.2.27
Gene Ontology:  GO:0046872|GO:0051865|GO:0016567|GO:0061630
PubMed:  19489725|11007473|22154517
SCOP:  3000160

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
zf-RING_5 pfam14634
zinc-RING finger domain;
6-45 9.13e-08

zinc-RING finger domain;


:

Pssm-ID: 434085 [Multi-domain]  Cd Length: 43  Bit Score: 47.42  E-value: 9.13e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1845970703   6 CNHCGIKP-NQTKLYLTACGHVFCQNCTKAAFNS-QCYLCKK 45
Cdd:pfam14634   2 CNKCFKELsKTRPFYLTSCGHIFCEECLTRLLQErQCPICKK 43
PRK00409 super family cl29770
recombination and DNA strand exchange inhibitor protein; Reviewed
 76-166 1.79e-03

recombination and DNA strand exchange inhibitor protein; Reviewed


The actual alignment was detected with superfamily member PRK00409:

Pssm-ID: 234750 [Multi-domain]  Cd Length: 782  Bit Score: 39.04  E-value: 1.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845970703  76 NELKQVVA-FQAKQREiyVKCKNAEA---KKDTERFAEARSKHVEKTQEIEKRKKAFLEDNVK--LKNAKEEKNQLmarL 149
Cdd:PRK00409  516 EKLNELIAsLEELERE--LEQKAEEAealLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQqaIKEAKKEADEI---I 590

                          90
                  ....*....|....*..
gi 1845970703 150 KELREQPSQNLSVNKRR 166
Cdd:PRK00409  591 KELRQLQKGGYASVKAH 607
 
Name Accession Description Interval E-value
zf-RING_5 pfam14634
zinc-RING finger domain;
6-45 9.13e-08

zinc-RING finger domain;


Pssm-ID: 434085 [Multi-domain]  Cd Length: 43  Bit Score: 47.42  E-value: 9.13e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1845970703   6 CNHCGIKP-NQTKLYLTACGHVFCQNCTKAAFNS-QCYLCKK 45
Cdd:pfam14634   2 CNKCFKELsKTRPFYLTSCGHIFCEECLTRLLQErQCPICKK 43
RING-HC_RNF212 cd16746
RING finger, HC subclass, found in RING finger protein 212 (RNF212) and similar proteins; ...
 3-46 2.04e-06

RING finger, HC subclass, found in RING finger protein 212 (RNF212) and similar proteins; RNF212 is a dosage-sensitive regulator of crossing-over during mammalian meiosis. It plays a central role in designating crossover sites and coupling chromosome synapsis to the formation of crossover-specific recombination complexes. It also functions as an E3 ligase for SUMO modification. RNF212 contains an N-terminal C3HC4-type RING-HC finger.


Pssm-ID: 438404  Cd Length: 48  Bit Score: 43.58  E-value: 2.04e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1845970703   3 WIQCNHCGIKP--NQTKLYLTACGHVFCQNCTKAAFNSQCYLCKKP 46
Cdd:cd16746     1 RVFCNFCFQQPrpNCPSFILTNCGHVVCEACLQKGKKNECLVCKAP 46
PRK00409 PRK00409
recombination and DNA strand exchange inhibitor protein; Reviewed
 76-166 1.79e-03

recombination and DNA strand exchange inhibitor protein; Reviewed


Pssm-ID: 234750 [Multi-domain]  Cd Length: 782  Bit Score: 39.04  E-value: 1.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845970703  76 NELKQVVA-FQAKQREiyVKCKNAEA---KKDTERFAEARSKHVEKTQEIEKRKKAFLEDNVK--LKNAKEEKNQLmarL 149
Cdd:PRK00409  516 EKLNELIAsLEELERE--LEQKAEEAealLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQqaIKEAKKEADEI---I 590

                          90
                  ....*....|....*..
gi 1845970703 150 KELREQPSQNLSVNKRR 166
Cdd:PRK00409  591 KELRQLQKGGYASVKAH 607
 
Name Accession Description Interval E-value
zf-RING_5 pfam14634
zinc-RING finger domain;
6-45 9.13e-08

zinc-RING finger domain;


Pssm-ID: 434085 [Multi-domain]  Cd Length: 43  Bit Score: 47.42  E-value: 9.13e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1845970703   6 CNHCGIKP-NQTKLYLTACGHVFCQNCTKAAFNS-QCYLCKK 45
Cdd:pfam14634   2 CNKCFKELsKTRPFYLTSCGHIFCEECLTRLLQErQCPICKK 43
RING-HC_RNF212 cd16746
RING finger, HC subclass, found in RING finger protein 212 (RNF212) and similar proteins; ...
 3-46 2.04e-06

RING finger, HC subclass, found in RING finger protein 212 (RNF212) and similar proteins; RNF212 is a dosage-sensitive regulator of crossing-over during mammalian meiosis. It plays a central role in designating crossover sites and coupling chromosome synapsis to the formation of crossover-specific recombination complexes. It also functions as an E3 ligase for SUMO modification. RNF212 contains an N-terminal C3HC4-type RING-HC finger.


Pssm-ID: 438404  Cd Length: 48  Bit Score: 43.58  E-value: 2.04e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1845970703   3 WIQCNHCGIKP--NQTKLYLTACGHVFCQNCTKAAFNSQCYLCKKP 46
Cdd:cd16746     1 RVFCNFCFQQPrpNCPSFILTNCGHVVCEACLQKGKKNECLVCKAP 46
RING-HC_RNF212-like cd16560
RING finger, HC subclass, found in RING finger proteins RNF212, RNF212B and similar proteins; ...
 4-44 4.07e-05

RING finger, HC subclass, found in RING finger proteins RNF212, RNF212B and similar proteins; This subfamily includes RING finger protein RNF212, RNF212B, and their homologs. RNF212 is a dosage-sensitive regulator of crossing-over during mammalian meiosis. It plays a central role in designating crossover sites and coupling chromosome synapsis to the formation of crossover-specific recombination complexes. It also functions as an E3 ligase for small ubiquitin-related modifier (SUMO) modification. RNF212B shows high sequence similarity with RNF212, but its biological function remains unclear. Members of this subfamily contain an N-terminal C3HC4-type RING-HC finger. Also included are two homologs of RNF212, meiotic procrossover factors Zip3 and ZHP-3, which have been identified in Saccharomyces cerevisiae and Caenorhabditis elegans, respectively. Budding yeast Zip3 is a small ubiquitin-related modifier (SUMO) E3 ligase implicated in the SUMO pathway of post-translational modification. It sumoylates chromosome axis proteins, thus promoting synaptonemal complex polymerization. It also acts as an Smt3 E3 ligase. Zip3 includes a SUMO Interacting Motif (SIM) and a modified C3HCHC2-type RING-HC finger that are important for Zip3 in vitro E3 ligase activity and necessary for SC polymerization and correct sporulation. ZHP-3 acts at crossovers to couple meiotic recombination with synaptonemal complex disassembly and chiasma formation in Caenorhabditis elegans. It possesses a C3HC4-type RING-HC finger.


Pssm-ID: 438222  Cd Length: 42  Bit Score: 39.83  E-value: 4.07e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1845970703   4 IQCNHCGIKPNQT-KLYLTACGHVFCQNCTKAAFNSQCYLCK 44
Cdd:cd16560     1 VHCNTCFQLPGDTsKFFLTSCGHIYCDACVGKGKRNKCKICG 42
RING-HC_LONFs_rpt2 cd16514
second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger ...
 21-47 4.59e-04

second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger protein family; The LON peptidase N-terminal domain and RING finger protein family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192, RNF192, or neuroblastoma apoptosis-related protease), LONRF3 (also known as RING finger protein 127 or RNF127), which are characterized by containing two C3HC4-type RING-HC fingers, four tetratricopeptide (TPR) repeats, and an ATP-dependent protease La (LON) substrate-binding domain at the C-terminus. Their biological functions remain unclear. This model corresponds to the second RING-HC finger.


Pssm-ID: 438177 [Multi-domain]  Cd Length: 45  Bit Score: 36.86  E-value: 4.59e-04
                          10        20
                  ....*....|....*....|....*....
gi 1845970703  21 TACGHVFCQNCTKAAF--NSQCYLCKKPL 47
Cdd:cd16514    17 TPCGHTFCRACLERCLdhSPKCPLCRTSL 45
RING-HC_RNF212B cd16747
RING finger, HC subclass, found in RING finger protein 212B (RNF212B) and similar proteins; ...
 4-44 9.86e-04

RING finger, HC subclass, found in RING finger protein 212B (RNF212B) and similar proteins; RNF212B is an uncharacterized protein with high sequence similarity with RNF212, a dosage-sensitive regulator of crossing-over during mammalian meiosis. RNF212B contains an N-terminal C3HC4-type RING-HC finger.


Pssm-ID: 438405  Cd Length: 37  Bit Score: 35.85  E-value: 9.86e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1845970703   4 IQCNHCGIKPNQTkLYLTACGHVFCQNCTKAafnSQCYLCK 44
Cdd:cd16747     1 FHCNKCFRRDGAS-FFITSCGHIFCEKCIKA---EKCTVCG 37
PRK00409 PRK00409
recombination and DNA strand exchange inhibitor protein; Reviewed
 76-166 1.79e-03

recombination and DNA strand exchange inhibitor protein; Reviewed


Pssm-ID: 234750 [Multi-domain]  Cd Length: 782  Bit Score: 39.04  E-value: 1.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1845970703  76 NELKQVVA-FQAKQREiyVKCKNAEA---KKDTERFAEARSKHVEKTQEIEKRKKAFLEDNVK--LKNAKEEKNQLmarL 149
Cdd:PRK00409  516 EKLNELIAsLEELERE--LEQKAEEAealLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQqaIKEAKKEADEI---I 590

                          90
                  ....*....|....*..
gi 1845970703 150 KELREQPSQNLSVNKRR 166
Cdd:PRK00409  591 KELRQLQKGGYASVKAH 607
RING-HC_CeBARD1-like cd23143
RING finger, HC subclass, found in Caenorhabditis elegans BRCA1-associated RING domain protein ...
 4-47 3.25e-03

RING finger, HC subclass, found in Caenorhabditis elegans BRCA1-associated RING domain protein 1 (CeBARD1) and similar proteins; CeBARD1, also called Ce-BRD-1, Cebrd-1, or RING-type E3 ubiquitin transferase BARD1, is a constituent of the CeBCD complex that possesses E3 ubiquitin-protein ligase activity. It plays a role in triggering cellular responses at damage sites in response to DNA damage that may be induced by ionizing radiation. It protects against chromosome non-disjunction and nuclear fragmentation during meiotic double-strand break repair to ensure sister chromatid recombination and aid chromosome stability. CeBARD1 contains a typical C3HC4-type RING-HC finger.


Pssm-ID: 438505 [Multi-domain]  Cd Length: 47  Bit Score: 34.83  E-value: 3.25e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1845970703   4 IQCNHCGiKPNQTKLYLTACGHVFCQNCTKAAFNSQ--CYLCKKPL 47
Cdd:cd23143     2 IECVICS-EPQIDTFLLSSCGHIYCWECFTEFIEKRhmCPSCRFPL 46
RING-HC_MAT1 cd16517
RING finger, HC subclass, found in RING finger protein MAT1; MAT1, also known as ...
 17-48 5.89e-03

RING finger, HC subclass, found in RING finger protein MAT1; MAT1, also known as CDK-activating kinase assembly factor MAT1, CDK7/cyclin-H assembly factor, cyclin-G1-interacting protein, menage a trois, RING finger protein 66 (RNF66), p35, or p36, is involved in cell cycle control and in RNA transcription by RNA polymerase II. It associates primarily with the catalytic subunit cyclin-dependent kinase 7 (CDK7) and the regulatory subunit cyclin H to form the CDK-activating kinase (CAK) complex that can further associate with the core-TFIIH to form the transcription factor IIH (TFIIH) basal transcription/DNA repair factor, which activates RNA polymerase II by serine phosphorylation of the repetitive C-terminal domain (CTD) of its large subunit (POLR2A), allowing its escape from the promoter, and elongation of the transcripts. MAT1 contains an N-terminal C3HC4-type RING-HC finger, a central coiled coil domain, and a C-terminal domain rich in hydrophobic residues.


Pssm-ID: 438180 [Multi-domain]  Cd Length: 55  Bit Score: 34.35  E-value: 5.89e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1845970703  17 KLYLTACGHVFCQNCTKAAF---NSQCYLCKKPLK 48
Cdd:cd16517    17 KLMVNVCGHTLCESCVDLLFvrgSGPCPECGTPLR 51
RING-HC_HLTF cd16509
RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar ...
 20-52 6.77e-03

RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins; HLTF, also known as DNA-binding protein/plasminogen activator inhibitor 1 regulator, HIP116, RING finger protein 80, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3, or sucrose nonfermenting protein 2-like 3, is a yeast RAD5 homolog found in mammals. It has both E3 ubiquitin ligase and DNA helicase activities, and plays a pivotal role in the template-switching pathway of DNA damage tolerance. It is involved in Lys-63-linked poly-ubiquitination of proliferating cell nuclear antigen (PCNA) at Lys-164 and in the regulation of DNA damage tolerance. It shows double-stranded DNA translocase activity with 3'-5' polarity, thereby facilitating regression of the replication fork. HLTF contains an N-terminal HIRAN (HIP116 and RAD5 N-terminal) domain, a SWI/SNF helicase domain that is divided into N- and C-terminal parts by an insertion of a C3HC4-type RING-HC finger involved in the poly-ubiquitination of PCNA.


Pssm-ID: 438172 [Multi-domain]  Cd Length: 53  Bit Score: 33.82  E-value: 6.77e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1845970703  20 LTACGHVFCQNC---TKAAFNSQCYLCKKPLKVDEI 52
Cdd:cd16509    18 ITPCAHVFCRRCiceVIQREKAKCPMCRAPLSASDL 53
RING-HC_PEX2 cd16526
RING finger, HC subclass, found in peroxin-2 (PEX2) and similar proteins; PEX2, also known as ...
 5-36 9.23e-03

RING finger, HC subclass, found in peroxin-2 (PEX2) and similar proteins; PEX2, also known as peroxisome biogenesis factor 2, 35 kDa peroxisomal membrane protein, peroxisomal membrane protein 3, peroxisome assembly factor 1 (PAF-1), or RING finger protein 72 (RNF72), is an integral peroxisomal membrane protein with two transmembrane regions and a C3HC4-type RING-HC finger within its cytoplasmically exposed C-terminus. It may be involved in the biogenesis of peroxisomes, as well as in peroxisomal matrix protein import. Mutations in the PEX2 gene are the primary defect in a subset of patients with Zellweger syndrome and related peroxisome biogenesis disorders. Moreover, PEX2 functions as an E3-ubiquitin ligase that mediates the UBC4-dependent polyubiquitination of PEX5, a key player in peroxisomal matrix protein import, to control PEX5 receptor recycling or degradation.


Pssm-ID: 438189 [Multi-domain]  Cd Length: 49  Bit Score: 33.51  E-value: 9.23e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1845970703   5 QCNHCGIKPNQTKlYLTACGHVFCQNCTKAAF 36
Cdd:cd16526     3 ECAICGEWPTNNP-YSTGCGHVYCYYCIKSNL 33
 
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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