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Conserved domains on  [gi|499411834|ref|WP_011099301|]
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Holliday junction resolvase RuvX [Clostridium tetani]

Protein Classification

RuvX/YqgF family protein( domain architecture ID 10002777)

RuvX/YqgF family protein such as Holliday junction resolvase RuvX, which acts as a dimer, or the monomeric pre-16S rRNA-processing nuclease YqgF, which was shown to process the 5' end of pre-16S rRNA within 70S ribosomes in vitro

EC:  3.1.-.-
Gene Ontology:  GO:0004518|GO:0000967

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YqgF COG0816
YqgF/RuvX protein, pre-16S rRNA maturation RNase/Holliday junction resolvase/anti-termination ...
 1-134 7.28e-70

YqgF/RuvX protein, pre-16S rRNA maturation RNase/Holliday junction resolvase/anti-termination factor [Translation, ribosomal structure and biogenesis, Replication, recombination and repair, Transcription];


:

Pssm-ID: 440578  Cd Length: 136  Bit Score: 206.07  E-value: 7.28e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499411834   1 MRILGLDVGDRTIGVAISDPLGWTAQGVKTIKRSNLKNDIKEIEDICNEYKVDKIVSGLPKNMNGTLGPQSEKVTEFCDI 80
Cdd:COG0816    3 GRILGLDVGTKRIGVAVSDPLGIIATPLETIKRKKGEPDLARLAKLIKEWEVDALVVGLPLNMDGSEGPRAQRARKFARR 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 499411834  81 LKKELEKEIIMWDERLTTVAAHKAMIEGDLSRAKRKKIVDKIAAIYILQGYLDS 134
Cdd:COG0816   83 LAGRFGLPVELVDERLTTVEAERALIEAGVSRKKRKGVIDQIAAVIILQSYLDS 136
 
Name Accession Description Interval E-value
YqgF COG0816
YqgF/RuvX protein, pre-16S rRNA maturation RNase/Holliday junction resolvase/anti-termination ...
 1-134 7.28e-70

YqgF/RuvX protein, pre-16S rRNA maturation RNase/Holliday junction resolvase/anti-termination factor [Translation, ribosomal structure and biogenesis, Replication, recombination and repair, Transcription];


Pssm-ID: 440578  Cd Length: 136  Bit Score: 206.07  E-value: 7.28e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499411834   1 MRILGLDVGDRTIGVAISDPLGWTAQGVKTIKRSNLKNDIKEIEDICNEYKVDKIVSGLPKNMNGTLGPQSEKVTEFCDI 80
Cdd:COG0816    3 GRILGLDVGTKRIGVAVSDPLGIIATPLETIKRKKGEPDLARLAKLIKEWEVDALVVGLPLNMDGSEGPRAQRARKFARR 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 499411834  81 LKKELEKEIIMWDERLTTVAAHKAMIEGDLSRAKRKKIVDKIAAIYILQGYLDS 134
Cdd:COG0816   83 LAGRFGLPVELVDERLTTVEAERALIEAGVSRKKRKGVIDQIAAVIILQSYLDS 136
PRK00109 PRK00109
Holliday junction resolvase RuvX;
1-134 5.74e-65

Holliday junction resolvase RuvX;


Pssm-ID: 234639  Cd Length: 138  Bit Score: 193.83  E-value: 5.74e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499411834   1 MRILGLDVGDRTIGVAISDPLGWTAQGVKTIKRSNLKNDIKEIEDICNEYKVDKIVSGLPKNMNGTLGPQSEKVTEFCDI 80
Cdd:PRK00109   4 GRILGLDVGTKRIGVAVSDPLGGTAQPLETIKRNNGTPDWDRLEKLIKEWQPDGLVVGLPLNMDGTEGPRTERARKFANR 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 499411834  81 LKKELEKEIIMWDERLTTVAAHKAMIEGDLSRAKRKKIVDKIAAIYILQGYLDS 134
Cdd:PRK00109  84 LEGRFGLPVVLVDERLSTVEAERALADVGSRKKLRKGVIDSLAAVIILQSYLDS 137
RuvX pfam03652
Holliday junction resolvase; The central intermediate formed during mitotic and meiotic ...
 1-134 2.16e-64

Holliday junction resolvase; The central intermediate formed during mitotic and meiotic recombination is a four stranded DNA structure, also known as the Holliday junction (HJ), and its efficient resolution is essential for proper segregation of chromosomes. Resolution of HJs is mediated by a diverse group of DNA structure specific endonucleases known as Holliday junction resolvases (HJR). This entry is specific for RuvX also known as YqgF a family of nucleases which resolves the Holliday junction intermediates in genetic recombination. Studies carried out in M. tuberculosis, have shown that YqgF/RuvX is a genuine HJR analogous to RuvC from E. coli. Furthermore, a single cysteine present in M. tuberculosis RuvX was found to be required for disulfide-bond mediated intermolecular dimerization and HJ resolution activity, suggesting that M. tuberculosis RuvX has adapted its YqgF protein to function like a typical RuvC family HJR.


Pssm-ID: 461005  Cd Length: 134  Bit Score: 192.34  E-value: 2.16e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499411834    1 MRILGLDVGDRTIGVAISDPLGWTAQGVKTIKRSNLKNDIKEIEDICNEYKVDKIVSGLPKNMNGTLGPQSEKVTEFCDI 80
Cdd:pfam03652   1 MRILGLDFGTKRIGVAVSDPLGITASPLETIPRKNGEADLAELKELIKEWQPDAIVVGLPLNMDGSEGERTERVRKFARR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 499411834   81 LKKELEKEIIMWDERLTTVAAHKAMIEGDLSRAKRKKIVDKIAAIYILQGYLDS 134
Cdd:pfam03652  81 LKKRFGLPVELVDERLSTVEAERRLIEAGVSRKKRKEVVDSIAAVIILQSYLDS 134
YqgF cd16964
putative pre-16S rRNA nuclease YqgF and RuvX family; Escherichia coli YqgF has been shown to ...
 3-134 2.98e-60

putative pre-16S rRNA nuclease YqgF and RuvX family; Escherichia coli YqgF has been shown to act as a pre-16S rRNA nuclease, presumably as a monomer. It is involved in the processing of pre-16S rRNA during ribosome maturation. The RuvX gene product from Mycobacterium tuberculosis was shown to act, in a dimeric form, as a Holliday junction resolvase (HJR). HJRs endonucleases specifically resolve Holliday junction DNA intermediates during homologous recombination. Holliday junctions are formed by the reciprocal exchange of strands between two DNA duplexes. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi; they may form homodimers and display structural similarity to RNase H and Hsp70.


Pssm-ID: 438564  Cd Length: 132  Bit Score: 181.91  E-value: 2.98e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499411834   3 ILGLDVGDRTIGVAISDPLGWTAQGVKTIKRSNLKNDIKEIEDICNEYKVDKIVSGLPKNMNGTLGPQSEKVTEFCDILK 82
Cdd:cd16964    1 ILGIDYGTKRIGLAISDPLGIIASPLETIERKNLEKLLEELKKIIKEEKIEKIVVGLPLNMDGTESEQAEKVRKFAEKLK 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 499411834  83 KELEKEIIMWDERLTTVAAHKAMIEGDLSRAKRKKIVDKIAAIYILQGYLDS 134
Cdd:cd16964   81 KRFGLPVVLVDERLTTKEAERILREAGKKRKKRKKKIDALAAAIILQSYLDS 132
RNAse_H_YqgF TIGR00250
putative transcription antitermination factor YqgF; This protein family, which exhibits an ...
 4-133 7.36e-47

putative transcription antitermination factor YqgF; This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC. [Unknown function, General]


Pssm-ID: 129352  Cd Length: 130  Bit Score: 148.05  E-value: 7.36e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499411834    4 LGLDVGDRTIGVAISDPLGWTAQGVKTIKRSNLKNDIKEIEDICNEYKVDKIVSGLPKNMNGTLGPQSEKVTEFCDILKK 83
Cdd:TIGR00250   1 LGLDFGTKSIGVAGQDITGWTAQGIPTIKAQDGEPDWSRIEELLKEWTPDKIVVGLPLNMDGTEGPLTERAQKFANRLEG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 499411834   84 ELEKEIIMWDERLTTVAAHKAMIEGDLSRAKRKKIVDKIAAIYILQGYLD 133
Cdd:TIGR00250  81 RFGVPVVLWDERLSTVEAESGLFARGGFRALRKGKIDKAAAVIILQSYLD 130
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 1-101 2.02e-35

Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.


Pssm-ID: 128971  Cd Length: 99  Bit Score: 117.67  E-value: 2.02e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499411834     1 MRILGLDVGDRTIGVAISDPLGWTAQGVKTIKRSNLKNDIKEIEDICNEYKVDKIVSGLPKNMNGTLGPQSEKvtEFCDI 80
Cdd:smart00732   1 KRVLGLDPGRKGIGVAVVDETGKLADPLEVIPRTNKEADAARLKKLIKKYQPDLIVIGLPLNMNGTASRETEE--AFAEL 78

                           90       100
                   ....*....|....*....|.
gi 499411834    81 LKKELEKEIIMWDERLTTVAA 101
Cdd:smart00732  79 LKERFNLPVVLVDERLATVYA 99
 
Name Accession Description Interval E-value
YqgF COG0816
YqgF/RuvX protein, pre-16S rRNA maturation RNase/Holliday junction resolvase/anti-termination ...
 1-134 7.28e-70

YqgF/RuvX protein, pre-16S rRNA maturation RNase/Holliday junction resolvase/anti-termination factor [Translation, ribosomal structure and biogenesis, Replication, recombination and repair, Transcription];


Pssm-ID: 440578  Cd Length: 136  Bit Score: 206.07  E-value: 7.28e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499411834   1 MRILGLDVGDRTIGVAISDPLGWTAQGVKTIKRSNLKNDIKEIEDICNEYKVDKIVSGLPKNMNGTLGPQSEKVTEFCDI 80
Cdd:COG0816    3 GRILGLDVGTKRIGVAVSDPLGIIATPLETIKRKKGEPDLARLAKLIKEWEVDALVVGLPLNMDGSEGPRAQRARKFARR 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 499411834  81 LKKELEKEIIMWDERLTTVAAHKAMIEGDLSRAKRKKIVDKIAAIYILQGYLDS 134
Cdd:COG0816   83 LAGRFGLPVELVDERLTTVEAERALIEAGVSRKKRKGVIDQIAAVIILQSYLDS 136
PRK00109 PRK00109
Holliday junction resolvase RuvX;
1-134 5.74e-65

Holliday junction resolvase RuvX;


Pssm-ID: 234639  Cd Length: 138  Bit Score: 193.83  E-value: 5.74e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499411834   1 MRILGLDVGDRTIGVAISDPLGWTAQGVKTIKRSNLKNDIKEIEDICNEYKVDKIVSGLPKNMNGTLGPQSEKVTEFCDI 80
Cdd:PRK00109   4 GRILGLDVGTKRIGVAVSDPLGGTAQPLETIKRNNGTPDWDRLEKLIKEWQPDGLVVGLPLNMDGTEGPRTERARKFANR 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 499411834  81 LKKELEKEIIMWDERLTTVAAHKAMIEGDLSRAKRKKIVDKIAAIYILQGYLDS 134
Cdd:PRK00109  84 LEGRFGLPVVLVDERLSTVEAERALADVGSRKKLRKGVIDSLAAVIILQSYLDS 137
RuvX pfam03652
Holliday junction resolvase; The central intermediate formed during mitotic and meiotic ...
 1-134 2.16e-64

Holliday junction resolvase; The central intermediate formed during mitotic and meiotic recombination is a four stranded DNA structure, also known as the Holliday junction (HJ), and its efficient resolution is essential for proper segregation of chromosomes. Resolution of HJs is mediated by a diverse group of DNA structure specific endonucleases known as Holliday junction resolvases (HJR). This entry is specific for RuvX also known as YqgF a family of nucleases which resolves the Holliday junction intermediates in genetic recombination. Studies carried out in M. tuberculosis, have shown that YqgF/RuvX is a genuine HJR analogous to RuvC from E. coli. Furthermore, a single cysteine present in M. tuberculosis RuvX was found to be required for disulfide-bond mediated intermolecular dimerization and HJ resolution activity, suggesting that M. tuberculosis RuvX has adapted its YqgF protein to function like a typical RuvC family HJR.


Pssm-ID: 461005  Cd Length: 134  Bit Score: 192.34  E-value: 2.16e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499411834    1 MRILGLDVGDRTIGVAISDPLGWTAQGVKTIKRSNLKNDIKEIEDICNEYKVDKIVSGLPKNMNGTLGPQSEKVTEFCDI 80
Cdd:pfam03652   1 MRILGLDFGTKRIGVAVSDPLGITASPLETIPRKNGEADLAELKELIKEWQPDAIVVGLPLNMDGSEGERTERVRKFARR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 499411834   81 LKKELEKEIIMWDERLTTVAAHKAMIEGDLSRAKRKKIVDKIAAIYILQGYLDS 134
Cdd:pfam03652  81 LKKRFGLPVELVDERLSTVEAERRLIEAGVSRKKRKEVVDSIAAVIILQSYLDS 134
YqgF cd16964
putative pre-16S rRNA nuclease YqgF and RuvX family; Escherichia coli YqgF has been shown to ...
 3-134 2.98e-60

putative pre-16S rRNA nuclease YqgF and RuvX family; Escherichia coli YqgF has been shown to act as a pre-16S rRNA nuclease, presumably as a monomer. It is involved in the processing of pre-16S rRNA during ribosome maturation. The RuvX gene product from Mycobacterium tuberculosis was shown to act, in a dimeric form, as a Holliday junction resolvase (HJR). HJRs endonucleases specifically resolve Holliday junction DNA intermediates during homologous recombination. Holliday junctions are formed by the reciprocal exchange of strands between two DNA duplexes. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi; they may form homodimers and display structural similarity to RNase H and Hsp70.


Pssm-ID: 438564  Cd Length: 132  Bit Score: 181.91  E-value: 2.98e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499411834   3 ILGLDVGDRTIGVAISDPLGWTAQGVKTIKRSNLKNDIKEIEDICNEYKVDKIVSGLPKNMNGTLGPQSEKVTEFCDILK 82
Cdd:cd16964    1 ILGIDYGTKRIGLAISDPLGIIASPLETIERKNLEKLLEELKKIIKEEKIEKIVVGLPLNMDGTESEQAEKVRKFAEKLK 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 499411834  83 KELEKEIIMWDERLTTVAAHKAMIEGDLSRAKRKKIVDKIAAIYILQGYLDS 134
Cdd:cd16964   81 KRFGLPVVLVDERLTTKEAERILREAGKKRKKRKKKIDALAAAIILQSYLDS 132
RNAse_H_YqgF TIGR00250
putative transcription antitermination factor YqgF; This protein family, which exhibits an ...
 4-133 7.36e-47

putative transcription antitermination factor YqgF; This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC. [Unknown function, General]


Pssm-ID: 129352  Cd Length: 130  Bit Score: 148.05  E-value: 7.36e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499411834    4 LGLDVGDRTIGVAISDPLGWTAQGVKTIKRSNLKNDIKEIEDICNEYKVDKIVSGLPKNMNGTLGPQSEKVTEFCDILKK 83
Cdd:TIGR00250   1 LGLDFGTKSIGVAGQDITGWTAQGIPTIKAQDGEPDWSRIEELLKEWTPDKIVVGLPLNMDGTEGPLTERAQKFANRLEG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 499411834   84 ELEKEIIMWDERLTTVAAHKAMIEGDLSRAKRKKIVDKIAAIYILQGYLD 133
Cdd:TIGR00250  81 RFGVPVVLWDERLSTVEAESGLFARGGFRALRKGKIDKAAAVIILQSYLD 130
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 1-101 2.02e-35

Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions.


Pssm-ID: 128971  Cd Length: 99  Bit Score: 117.67  E-value: 2.02e-35
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499411834     1 MRILGLDVGDRTIGVAISDPLGWTAQGVKTIKRSNLKNDIKEIEDICNEYKVDKIVSGLPKNMNGTLGPQSEKvtEFCDI 80
Cdd:smart00732   1 KRVLGLDPGRKGIGVAVVDETGKLADPLEVIPRTNKEADAARLKKLIKKYQPDLIVIGLPLNMNGTASRETEE--AFAEL 78

                           90       100
                   ....*....|....*....|.
gi 499411834    81 LKKELEKEIIMWDERLTTVAA 101
Cdd:smart00732  79 LKERFNLPVVLVDERLATVYA 99
RuvC-like cd00529
Crossover junction endodeoxyribonuclease RuvC and similar proteins; The RuvC-like family ...
 3-68 8.06e-09

Crossover junction endodeoxyribonuclease RuvC and similar proteins; The RuvC-like family consists of bacterial RuvC, fungal Cruciform cutting endonuclease 1 (CCE1), bacterial YqgF and monokaryotic chloroplast 1 protein (MOC1). RuvC, CCE1 and MOC1 are Holliday junction resolvases (HJRs), endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. RuvC 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. CCE1 is a HJR specific for 4-way junctions; it is involved in the maintenance of mitochondrial DNA. Escherichia coli YqgF has been shown to act as a pre-16S rRNA nuclease, presumably as a monomer. It is involved in the processing of pre-16S rRNA during ribosome maturation. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi. RuvC and its orthologs are homodimers and display structural similarity to RNase H and Hsp70.


Pssm-ID: 438561  Cd Length: 110  Bit Score: 50.11  E-value: 8.06e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499411834   3 ILGLDVGDRTIGVAISDPLGWTAQGVKTIK-------RSNLKNDIKEIEDICNEYKVDKIVSGLPKNMNGTLG 68
Cdd:cd00529    1 VLGIDPGTKSLGLAVLSQNGVTALQVEVIKtlevlvgPSRGRLDAARIVELLKEFQPDTIAVEQQFNYPGTGG 73
 
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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