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Conserved domains on  [gi|2542083902|ref|WP_298092459|]
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Holliday junction resolvase RuvX [Sphingomonas sp.]

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

 Zoom to residue level

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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 ...
 15-148 4.04e-55

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: 169.48  E-value: 4.04e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2542083902  15 SGGRLLGLDVGTKTIGTALCDAGWSFASPATLVRRTKFTKDKAQLAELIASQSVKGLVIGLPLNLDGSESPRSQSTRAFA 94
Cdd:COG0816     1 RMGRILGLDVGTKRIGVAVSDPLGIIATPLETIKRKKGEPDLARLAKLIKEWEVDALVVGLPLNMDGSEGPRAQRARKFA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2542083902  95 RNCEDL--GPILLWDERWSTVAVERIMIEQDMSRAKRAEKIDNFAAAHILQAAIDA 148
Cdd:COG0816    81 RRLAGRfgLPVELVDERLTTVEAERALIEAGVSRKKRKGVIDQIAAVIILQSYLDS 136
 
Name Accession Description Interval E-value
YqgF COG0816
YqgF/RuvX protein, pre-16S rRNA maturation RNase/Holliday junction resolvase/anti-termination ...
 15-148 4.04e-55

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: 169.48  E-value: 4.04e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2542083902  15 SGGRLLGLDVGTKTIGTALCDAGWSFASPATLVRRTKFTKDKAQLAELIASQSVKGLVIGLPLNLDGSESPRSQSTRAFA 94
Cdd:COG0816     1 RMGRILGLDVGTKRIGVAVSDPLGIIATPLETIKRKKGEPDLARLAKLIKEWEVDALVVGLPLNMDGSEGPRAQRARKFA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2542083902  95 RNCEDL--GPILLWDERWSTVAVERIMIEQDMSRAKRAEKIDNFAAAHILQAAIDA 148
Cdd:COG0816    81 RRLAGRfgLPVELVDERLTTVEAERALIEAGVSRKKRKGVIDQIAAVIILQSYLDS 136
RuvX pfam03652
Holliday junction resolvase; The central intermediate formed during mitotic and meiotic ...
 17-148 1.35e-49

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: 155.36  E-value: 1.35e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2542083902  17 GRLLGLDVGTKTIGTALCDAGWSFASPATLVRRTKFTKDKAQLAELIASQSVKGLVIGLPLNLDGSESPRSQSTRAFARN 96
Cdd:pfam03652   1 MRILGLDFGTKRIGVAVSDPLGITASPLETIPRKNGEADLAELKELIKEWQPDAIVVGLPLNMDGSEGERTERVRKFARR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2542083902  97 CEDLG--PILLWDERWSTVAVERIMIEQDMSRAKRAEKIDNFAAAHILQAAIDA 148
Cdd:pfam03652  81 LKKRFglPVELVDERLSTVEAERRLIEAGVSRKKRKEVVDSIAAVIILQSYLDS 134
PRK00109 PRK00109
Holliday junction resolvase RuvX;
14-149 1.55e-46

Holliday junction resolvase RuvX;


Pssm-ID: 234639  Cd Length: 138  Bit Score: 147.60  E-value: 1.55e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2542083902  14 PSGGRLLGLDVGTKTIGTALCDAGWSFASPATLVRRTKFTKDKAQLAELIASQSVKGLVIGLPLNLDGSESPRSQSTRAF 93
Cdd:PRK00109    1 MPSGRILGLDVGTKRIGVAVSDPLGGTAQPLETIKRNNGTPDWDRLEKLIKEWQPDGLVVGLPLNMDGTEGPRTERARKF 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2542083902  94 ARNCEDL--GPILLWDERWSTVAVERIMIEQDMSRAKRAEKIDNFAAAHILQAAIDAL 149
Cdd:PRK00109   81 ANRLEGRfgLPVVLVDERLSTVEAERALADVGSRKKLRKGVIDSLAAVIILQSYLDSL 138
YqgF cd16964
putative pre-16S rRNA nuclease YqgF and RuvX family; Escherichia coli YqgF has been shown to ...
 19-148 6.99e-45

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: 143.39  E-value: 6.99e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2542083902  19 LLGLDVGTKTIGTALCDAGWSFASPATLVRRTKFTKDKAQLAELIASQSVKGLVIGLPLNLDGSESPRSQSTRAFARNCE 98
Cdd:cd16964     1 ILGIDYGTKRIGLAISDPLGIIASPLETIERKNLEKLLEELKKIIKEEKIEKIVVGLPLNMDGTESEQAEKVRKFAEKLK 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2542083902  99 DLG--PILLWDERWSTVAVERIMIEQDMSRAKRAEKIDNFAAAHILQAAIDA 148
Cdd:cd16964    81 KRFglPVVLVDERLTTKEAERILREAGKKRKKRKKKIDALAAAIILQSYLDS 132
RNAse_H_YqgF TIGR00250
putative transcription antitermination factor YqgF; This protein family, which exhibits an ...
 20-147 2.07e-31

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: 109.14  E-value: 2.07e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2542083902  20 LGLDVGTKTIGTALCD-AGWSfASPATLVRRTKFTKDKAQLAELIASQSVKGLVIGLPLNLDGSESPRSQSTRAFARNCE 98
Cdd:TIGR00250   1 LGLDFGTKSIGVAGQDiTGWT-AQGIPTIKAQDGEPDWSRIEELLKEWTPDKIVVGLPLNMDGTEGPLTERAQKFANRLE 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2542083902  99 D-LG-PILLWDERWSTVAVERIMIEQDMSRAKRAEKIDNFAAAHILQAAID 147
Cdd:TIGR00250  80 GrFGvPVVLWDERLSTVEAESGLFARGGFRALRKGKIDKAAAVIILQSYLD 130
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 17-115 4.55e-27

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: 97.25  E-value: 4.55e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2542083902   17 GRLLGLDVGTKTIGTALCDAGWSFASPATLVRRTKFTKDKAQLAELIASQSVKGLVIGLPLNLDGSESPRSQstRAFARN 96
Cdd:smart00732   1 KRVLGLDPGRKGIGVAVVDETGKLADPLEVIPRTNKEADAARLKKLIKKYQPDLIVIGLPLNMNGTASRETE--EAFAEL 78

                           90       100
                   ....*....|....*....|.
gi 2542083902   97 CEDL--GPILLWDERWSTVAV 115
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 ...
 15-148 4.04e-55

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: 169.48  E-value: 4.04e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2542083902  15 SGGRLLGLDVGTKTIGTALCDAGWSFASPATLVRRTKFTKDKAQLAELIASQSVKGLVIGLPLNLDGSESPRSQSTRAFA 94
Cdd:COG0816     1 RMGRILGLDVGTKRIGVAVSDPLGIIATPLETIKRKKGEPDLARLAKLIKEWEVDALVVGLPLNMDGSEGPRAQRARKFA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2542083902  95 RNCEDL--GPILLWDERWSTVAVERIMIEQDMSRAKRAEKIDNFAAAHILQAAIDA 148
Cdd:COG0816    81 RRLAGRfgLPVELVDERLTTVEAERALIEAGVSRKKRKGVIDQIAAVIILQSYLDS 136
RuvX pfam03652
Holliday junction resolvase; The central intermediate formed during mitotic and meiotic ...
 17-148 1.35e-49

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: 155.36  E-value: 1.35e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2542083902  17 GRLLGLDVGTKTIGTALCDAGWSFASPATLVRRTKFTKDKAQLAELIASQSVKGLVIGLPLNLDGSESPRSQSTRAFARN 96
Cdd:pfam03652   1 MRILGLDFGTKRIGVAVSDPLGITASPLETIPRKNGEADLAELKELIKEWQPDAIVVGLPLNMDGSEGERTERVRKFARR 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2542083902  97 CEDLG--PILLWDERWSTVAVERIMIEQDMSRAKRAEKIDNFAAAHILQAAIDA 148
Cdd:pfam03652  81 LKKRFglPVELVDERLSTVEAERRLIEAGVSRKKRKEVVDSIAAVIILQSYLDS 134
PRK00109 PRK00109
Holliday junction resolvase RuvX;
14-149 1.55e-46

Holliday junction resolvase RuvX;


Pssm-ID: 234639  Cd Length: 138  Bit Score: 147.60  E-value: 1.55e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2542083902  14 PSGGRLLGLDVGTKTIGTALCDAGWSFASPATLVRRTKFTKDKAQLAELIASQSVKGLVIGLPLNLDGSESPRSQSTRAF 93
Cdd:PRK00109    1 MPSGRILGLDVGTKRIGVAVSDPLGGTAQPLETIKRNNGTPDWDRLEKLIKEWQPDGLVVGLPLNMDGTEGPRTERARKF 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2542083902  94 ARNCEDL--GPILLWDERWSTVAVERIMIEQDMSRAKRAEKIDNFAAAHILQAAIDAL 149
Cdd:PRK00109   81 ANRLEGRfgLPVVLVDERLSTVEAERALADVGSRKKLRKGVIDSLAAVIILQSYLDSL 138
YqgF cd16964
putative pre-16S rRNA nuclease YqgF and RuvX family; Escherichia coli YqgF has been shown to ...
 19-148 6.99e-45

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: 143.39  E-value: 6.99e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2542083902  19 LLGLDVGTKTIGTALCDAGWSFASPATLVRRTKFTKDKAQLAELIASQSVKGLVIGLPLNLDGSESPRSQSTRAFARNCE 98
Cdd:cd16964     1 ILGIDYGTKRIGLAISDPLGIIASPLETIERKNLEKLLEELKKIIKEEKIEKIVVGLPLNMDGTESEQAEKVRKFAEKLK 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2542083902  99 DLG--PILLWDERWSTVAVERIMIEQDMSRAKRAEKIDNFAAAHILQAAIDA 148
Cdd:cd16964    81 KRFglPVVLVDERLTTKEAERILREAGKKRKKRKKKIDALAAAIILQSYLDS 132
RNAse_H_YqgF TIGR00250
putative transcription antitermination factor YqgF; This protein family, which exhibits an ...
 20-147 2.07e-31

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: 109.14  E-value: 2.07e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2542083902  20 LGLDVGTKTIGTALCD-AGWSfASPATLVRRTKFTKDKAQLAELIASQSVKGLVIGLPLNLDGSESPRSQSTRAFARNCE 98
Cdd:TIGR00250   1 LGLDFGTKSIGVAGQDiTGWT-AQGIPTIKAQDGEPDWSRIEELLKEWTPDKIVVGLPLNMDGTEGPLTERAQKFANRLE 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2542083902  99 D-LG-PILLWDERWSTVAVERIMIEQDMSRAKRAEKIDNFAAAHILQAAID 147
Cdd:TIGR00250  80 GrFGvPVVLWDERLSTVEAESGLFARGGFRALRKGKIDKAAAVIILQSYLD 130
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 17-115 4.55e-27

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: 97.25  E-value: 4.55e-27
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2542083902   17 GRLLGLDVGTKTIGTALCDAGWSFASPATLVRRTKFTKDKAQLAELIASQSVKGLVIGLPLNLDGSESPRSQstRAFARN 96
Cdd:smart00732   1 KRVLGLDPGRKGIGVAVVDETGKLADPLEVIPRTNKEADAARLKKLIKKYQPDLIVIGLPLNMNGTASRETE--EAFAEL 78

                           90       100
                   ....*....|....*....|.
gi 2542083902   97 CEDL--GPILLWDERWSTVAV 115
Cdd:smart00732  79 LKERfnLPVVLVDERLATVYA 99
 
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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