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Conserved domains on  [gi|1938373637|ref|YP_009964095|]
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RuvC-like Holliday junction resolvase [Mycobacterium phage Rem711]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RuvC super family cl43282
Holliday junction resolvasome RuvABC endonuclease subunit RuvC [Replication, recombination and ...
 4-156 5.54e-09

Holliday junction resolvasome RuvABC endonuclease subunit RuvC [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG0817:

Pssm-ID: 440579  Cd Length: 152  Bit Score: 52.77  E-value: 5.54e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938373637   4 VMGIDSSLTRTGITVLTQDRNgvaRPKVLkDCGysLPDTAGFDESADRIVSQARTVARVLDKFPPALVLIEAMIPPKNAl 83
Cdd:COG0817     1 ILGIDPGLRRTGYGVIEVDGN---RLRLV-ASG--VIRTPPKLPLPERLLEIYEGLTELIEEYKPDEVAIEEVFFNKNP- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938373637  84 psyleRGALWYSlwyEFRA--------RNIPRALIQPTTLKAWATGYGRAEKEDILGEVSKW--WPAIPvANHDIADS-- 151
Cdd:COG0817    74 -----KSALKLG---QARGvallaaaqRGLPVAEYTPLQVKKAVTGYGRADKEQVQAMVKRLlgLDEIP-KPDDAADAla 144


                  ....*.
gi 1938373637 152 -AVCAA 156
Cdd:COG0817   145 iAICHA 150
 
Name Accession Description Interval E-value
RuvC COG0817
Holliday junction resolvasome RuvABC endonuclease subunit RuvC [Replication, recombination and ...
 4-156 5.54e-09

Holliday junction resolvasome RuvABC endonuclease subunit RuvC [Replication, recombination and repair];


Pssm-ID: 440579  Cd Length: 152  Bit Score: 52.77  E-value: 5.54e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938373637   4 VMGIDSSLTRTGITVLTQDRNgvaRPKVLkDCGysLPDTAGFDESADRIVSQARTVARVLDKFPPALVLIEAMIPPKNAl 83
Cdd:COG0817     1 ILGIDPGLRRTGYGVIEVDGN---RLRLV-ASG--VIRTPPKLPLPERLLEIYEGLTELIEEYKPDEVAIEEVFFNKNP- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938373637  84 psyleRGALWYSlwyEFRA--------RNIPRALIQPTTLKAWATGYGRAEKEDILGEVSKW--WPAIPvANHDIADS-- 151
Cdd:COG0817    74 -----KSALKLG---QARGvallaaaqRGLPVAEYTPLQVKKAVTGYGRADKEQVQAMVKRLlgLDEIP-KPDDAADAla 144


                  ....*.
gi 1938373637 152 -AVCAA 156
Cdd:COG0817   145 iAICHA 150
RuvC cd16962
Crossover junction endodeoxyribonuclease RuvC; Crossover junction endodeoxyribonuclease RuvC ...
 4-159 1.44e-08

Crossover junction endodeoxyribonuclease RuvC; Crossover junction endodeoxyribonuclease RuvC is also called Holliday junction resolvase RuvC. It is part of the RuvABC pathway in Escherichia coli and other Gram-negative bacteria that is involved in processing Holliday junctions, which are formed by the reciprocal exchange of strands between two DNA duplexes. Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. RuvC is thought to bind either on the open, DNA exposed face of a single RuvA tetramer, or to replace one of the two tetramers. Binding is proposed to be mediated by an unstructured loop on RuvC, which becomes structured on binding RuvA. RuvC can be bound to the complex in either orientation, therefore resolving Holliday junctions in either a horizontal or vertical manner. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the Escherichia coli HJR. RuvC and its orthologs are homodimers and display structural similarity to RNase H and Hsp70.


Pssm-ID: 438562  Cd Length: 152  Bit Score: 51.67  E-value: 1.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938373637   4 VMGIDSSLTRTGITVLTQDRNgvaRPKVLkDCGysLPDTAGFDESADRIVSQARTVARVLDKFPPALVLIEAMIP---PK 80
Cdd:cd16962     1 ILGIDPGLRRTGYGVIEVEGN---KLRLL-DYG--VIRTPSKLSLPERLKEIYDGLSELIEKYKPDEVAIEKLFFnknPK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938373637  81 NALPSYLERGALWYSLWYefraRNIPRALIQPTTLKAWATGYGRAEKEDI---------LGEVSKwwpaipvaNHDIADs 151
Cdd:cd16962    75 SALKLGQARGVILLAAAQ----AGLPVVEYTPRQVKQAVTGYGRADKEQVqymvkrllgLKEIPK--------PDDAAD- 141


                  ....*...
gi 1938373637 152 AVCAAMCA 159
Cdd:cd16962   142 ALAIALCH 149
RuvC pfam02075
Crossover junction endodeoxyribonuclease RuvC; This entry includes endodeoxyribonucleases ...
 4-158 9.01e-04

Crossover junction endodeoxyribonuclease RuvC; This entry includes endodeoxyribonucleases found in bacteria, such as RuvC. RuvC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli RuvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices. The Escherichia coli RuvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination. RuvC protein (EC:3.1.22.4) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo.


Pssm-ID: 366907  Cd Length: 148  Bit Score: 38.21  E-value: 9.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938373637   4 VMGIDSSLTRTGITVLTQDRNGVarpkVLKDCGYSLPDTagfDESADRIVSQARTVARVLDKFPPALVLIEAMIPPKN-- 81
Cdd:pfam02075   1 ILGIDPGSRKTGYGVIEHAGRQL----SYLTSGVIRTTS---DPLQERLLDVFDAVDEVIDRYQPDYVAIEQVFFAKNvd 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938373637  82 -ALPSYLERGALWYSLwyefRARNIPRALIQPTTLKAWATGYGRAEKEDILGEVSKWW--PAIPVANhDIADsAVCAAMC 158
Cdd:pfam02075  74 sALKLAQARGVAILAA----AERGISVAEYTPSQVKKAVTGNGKAEKEQVQHMVKRLLnlTAKPQPA-DAAD-ALAVAIT 147
 
Name Accession Description Interval E-value
RuvC COG0817
Holliday junction resolvasome RuvABC endonuclease subunit RuvC [Replication, recombination and ...
 4-156 5.54e-09

Holliday junction resolvasome RuvABC endonuclease subunit RuvC [Replication, recombination and repair];


Pssm-ID: 440579  Cd Length: 152  Bit Score: 52.77  E-value: 5.54e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938373637   4 VMGIDSSLTRTGITVLTQDRNgvaRPKVLkDCGysLPDTAGFDESADRIVSQARTVARVLDKFPPALVLIEAMIPPKNAl 83
Cdd:COG0817     1 ILGIDPGLRRTGYGVIEVDGN---RLRLV-ASG--VIRTPPKLPLPERLLEIYEGLTELIEEYKPDEVAIEEVFFNKNP- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938373637  84 psyleRGALWYSlwyEFRA--------RNIPRALIQPTTLKAWATGYGRAEKEDILGEVSKW--WPAIPvANHDIADS-- 151
Cdd:COG0817    74 -----KSALKLG---QARGvallaaaqRGLPVAEYTPLQVKKAVTGYGRADKEQVQAMVKRLlgLDEIP-KPDDAADAla 144


                  ....*.
gi 1938373637 152 -AVCAA 156
Cdd:COG0817   145 iAICHA 150
RuvC cd16962
Crossover junction endodeoxyribonuclease RuvC; Crossover junction endodeoxyribonuclease RuvC ...
 4-159 1.44e-08

Crossover junction endodeoxyribonuclease RuvC; Crossover junction endodeoxyribonuclease RuvC is also called Holliday junction resolvase RuvC. It is part of the RuvABC pathway in Escherichia coli and other Gram-negative bacteria that is involved in processing Holliday junctions, which are formed by the reciprocal exchange of strands between two DNA duplexes. Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. RuvC is thought to bind either on the open, DNA exposed face of a single RuvA tetramer, or to replace one of the two tetramers. Binding is proposed to be mediated by an unstructured loop on RuvC, which becomes structured on binding RuvA. RuvC can be bound to the complex in either orientation, therefore resolving Holliday junctions in either a horizontal or vertical manner. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the Escherichia coli HJR. RuvC and its orthologs are homodimers and display structural similarity to RNase H and Hsp70.


Pssm-ID: 438562  Cd Length: 152  Bit Score: 51.67  E-value: 1.44e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938373637   4 VMGIDSSLTRTGITVLTQDRNgvaRPKVLkDCGysLPDTAGFDESADRIVSQARTVARVLDKFPPALVLIEAMIP---PK 80
Cdd:cd16962     1 ILGIDPGLRRTGYGVIEVEGN---KLRLL-DYG--VIRTPSKLSLPERLKEIYDGLSELIEKYKPDEVAIEKLFFnknPK 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938373637  81 NALPSYLERGALWYSLWYefraRNIPRALIQPTTLKAWATGYGRAEKEDI---------LGEVSKwwpaipvaNHDIADs 151
Cdd:cd16962    75 SALKLGQARGVILLAAAQ----AGLPVVEYTPRQVKQAVTGYGRADKEQVqymvkrllgLKEIPK--------PDDAAD- 141


                  ....*...
gi 1938373637 152 AVCAAMCA 159
Cdd:cd16962   142 ALAIALCH 149
RuvC pfam02075
Crossover junction endodeoxyribonuclease RuvC; This entry includes endodeoxyribonucleases ...
 4-158 9.01e-04

Crossover junction endodeoxyribonuclease RuvC; This entry includes endodeoxyribonucleases found in bacteria, such as RuvC. RuvC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli RuvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices. The Escherichia coli RuvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination. RuvC protein (EC:3.1.22.4) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo.


Pssm-ID: 366907  Cd Length: 148  Bit Score: 38.21  E-value: 9.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938373637   4 VMGIDSSLTRTGITVLTQDRNGVarpkVLKDCGYSLPDTagfDESADRIVSQARTVARVLDKFPPALVLIEAMIPPKN-- 81
Cdd:pfam02075   1 ILGIDPGSRKTGYGVIEHAGRQL----SYLTSGVIRTTS---DPLQERLLDVFDAVDEVIDRYQPDYVAIEQVFFAKNvd 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938373637  82 -ALPSYLERGALWYSLwyefRARNIPRALIQPTTLKAWATGYGRAEKEDILGEVSKWW--PAIPVANhDIADsAVCAAMC 158
Cdd:pfam02075  74 sALKLAQARGVAILAA----AERGISVAEYTPSQVKKAVTGNGKAEKEQVQHMVKRLLnlTAKPQPA-DAAD-ALAVAIT 147
 
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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