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Conserved domains on  [gi|79317769|ref|NP_001031028|]
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Polynucleotidyl transferase, ribonuclease H-like superfamily protein [Arabidopsis thaliana]

Protein Classification

RuvX/YqgF family protein( domain architecture ID 13015107)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YqgF cd16964
putative pre-16S rRNA nuclease YqgF and RuvX family; Escherichia coli YqgF has been shown to ...
 84-212 2.01e-24

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: 94.47  E-value: 2.01e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79317769  84 LGVDLGLSRTGIAIS--KGYTVKPLTVLKSRG-QKLETRLLEIAEEEEADEFIIGLPRSSDGKETIQSNKIRSVAGRLAi 160
Cdd:cd16964   2 LGIDYGTKRIGLAISdpLGIIASPLETIERKNlEKLLEELKKIIKEEKIEKIVVGLPLNMDGTESEQAEKVRKFAEKLK- 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 79317769 161 qaAERGWRVYVFDEHGTTSEASDRMIVMGLSKSERQNRSDAYAAVILLERYF 212
Cdd:cd16964  81 --KRFGLPVVLVDERLTTKEAERILREAGKKRKKRKKKIDALAAAIILQSYL 130
 
Name Accession Description Interval E-value
YqgF cd16964
putative pre-16S rRNA nuclease YqgF and RuvX family; Escherichia coli YqgF has been shown to ...
 84-212 2.01e-24

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: 94.47  E-value: 2.01e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79317769  84 LGVDLGLSRTGIAIS--KGYTVKPLTVLKSRG-QKLETRLLEIAEEEEADEFIIGLPRSSDGKETIQSNKIRSVAGRLAi 160
Cdd:cd16964   2 LGIDYGTKRIGLAISdpLGIIASPLETIERKNlEKLLEELKKIIKEEKIEKIVVGLPLNMDGTESEQAEKVRKFAEKLK- 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 79317769 161 qaAERGWRVYVFDEHGTTSEASDRMIVMGLSKSERQNRSDAYAAVILLERYF 212
Cdd:cd16964  81 --KRFGLPVVLVDERLTTKEAERILREAGKKRKKRKKKIDALAAAIILQSYL 130
YqgF COG0816
YqgF/RuvX protein, pre-16S rRNA maturation RNase/Holliday junction resolvase/anti-termination ...
 84-212 2.43e-19

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: 81.26  E-value: 2.43e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79317769  84 LGVDLGLSRTGIAISK--GYTVKPLTVLKSR-GQKLETRLLEIAEEEEADEFIIGLPRSSDGKETIQSNKIRSVAGRLai 160
Cdd:COG0816   6 LGLDVGTKRIGVAVSDplGIIATPLETIKRKkGEPDLARLAKLIKEWEVDALVVGLPLNMDGSEGPRAQRARKFARRL-- 83

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 79317769 161 qAAERGWRVYVFDEHGTTSEASDRMIVMGLSKSERQNRSDAYAAVILLERYF 212
Cdd:COG0816  84 -AGRFGLPVELVDERLTTVEAERALIEAGVSRKKRKGVIDQIAAVIILQSYL 134
RuvX pfam03652
Holliday junction resolvase; The central intermediate formed during mitotic and meiotic ...
 84-214 6.51e-19

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: 79.86  E-value: 6.51e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79317769    84 LGVDLGLSRTGIAIS--KGYTVKPLTVL--KSRGQKLEtRLLEIAEEEEADEFIIGLPRSSDGKETIQSNKIRSVAGRLA 159
Cdd:pfam03652   4 LGLDFGTKRIGVAVSdpLGITASPLETIprKNGEADLA-ELKELIKEWQPDAIVVGLPLNMDGSEGERTERVRKFARRLK 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 79317769   160 iqaAERGWRVYVFDEHGTTSEASDRMIVMGLSKSERQNRSDAYAAVILLERYFST 214
Cdd:pfam03652  83 ---KRFGLPVELVDERLSTVEAERRLIEAGVSRKKRKEVVDSIAAVIILQSYLDS 134
PRK00109 PRK00109
Holliday junction resolvase RuvX;
84-212 6.90e-13

Holliday junction resolvase RuvX;


Pssm-ID: 234639  Cd Length: 138  Bit Score: 64.02  E-value: 6.90e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79317769   84 LGVDLGLSRTGIAIS--KGYTVKPLTVLKSRGQKLE-TRLLEIAEEEEADEFIIGLPRSSDGKETIQSNKIR----SVAG 156
Cdd:PRK00109   7 LGLDVGTKRIGVAVSdpLGGTAQPLETIKRNNGTPDwDRLEKLIKEWQPDGLVVGLPLNMDGTEGPRTERARkfanRLEG 86

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 79317769  157 RLAIQaaergwrVYVFDEHGTTSEASDRMIVMGLSKSERQNRSDAYAAVILLERYF 212
Cdd:PRK00109  87 RFGLP-------VVLVDERLSTVEAERALADVGSRKKLRKGVIDSLAAVIILQSYL 135
RNAse_H_YqgF TIGR00250
putative transcription antitermination factor YqgF; This protein family, which exhibits an ...
 84-212 1.99e-09

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: 54.45  E-value: 1.99e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79317769    84 LGVDLGLSRTGIAISK--GYTVKPLTVLK-SRGQKLETRLLEIAEEEEADEFIIGLPRSSDGKETIQSNKIRSVAGRLAI 160
Cdd:TIGR00250   1 LGLDFGTKSIGVAGQDitGWTAQGIPTIKaQDGEPDWSRIEELLKEWTPDKIVVGLPLNMDGTEGPLTERAQKFANRLEG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 79317769   161 QAaerGWRVYVFDEHGTTSEASDRMIVMGLSKSERQNRSDAYAAVILLERYF 212
Cdd:TIGR00250  81 RF---GVPVVLWDERLSTVEAESGLFARGGFRALRKGKIDKAAAVIILQSYL 129
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 84-181 2.10e-03

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: 36.78  E-value: 2.10e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79317769     84 LGVDLGLSRTGIAIS--KGYTVKPLTVLK-SRGQKLETRLLEIAEEEEADEFIIGLPRSSDGKETIQSNKI--RSVAGRL 158
Cdd:smart00732   4 LGLDPGRKGIGVAVVdeTGKLADPLEVIPrTNKEADAARLKKLIKKYQPDLIVIGLPLNMNGTASRETEEAfaELLKERF 83

                           90       100
                   ....*....|....*....|...
gi 79317769    159 AIQaaergwrVYVFDEHGTTSEA 181
Cdd:smart00732  84 NLP-------VVLVDERLATVYA 99
 
Name Accession Description Interval E-value
YqgF cd16964
putative pre-16S rRNA nuclease YqgF and RuvX family; Escherichia coli YqgF has been shown to ...
 84-212 2.01e-24

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: 94.47  E-value: 2.01e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79317769  84 LGVDLGLSRTGIAIS--KGYTVKPLTVLKSRG-QKLETRLLEIAEEEEADEFIIGLPRSSDGKETIQSNKIRSVAGRLAi 160
Cdd:cd16964   2 LGIDYGTKRIGLAISdpLGIIASPLETIERKNlEKLLEELKKIIKEEKIEKIVVGLPLNMDGTESEQAEKVRKFAEKLK- 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 79317769 161 qaAERGWRVYVFDEHGTTSEASDRMIVMGLSKSERQNRSDAYAAVILLERYF 212
Cdd:cd16964  81 --KRFGLPVVLVDERLTTKEAERILREAGKKRKKRKKKIDALAAAIILQSYL 130
YqgF COG0816
YqgF/RuvX protein, pre-16S rRNA maturation RNase/Holliday junction resolvase/anti-termination ...
 84-212 2.43e-19

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: 81.26  E-value: 2.43e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79317769  84 LGVDLGLSRTGIAISK--GYTVKPLTVLKSR-GQKLETRLLEIAEEEEADEFIIGLPRSSDGKETIQSNKIRSVAGRLai 160
Cdd:COG0816   6 LGLDVGTKRIGVAVSDplGIIATPLETIKRKkGEPDLARLAKLIKEWEVDALVVGLPLNMDGSEGPRAQRARKFARRL-- 83

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 79317769 161 qAAERGWRVYVFDEHGTTSEASDRMIVMGLSKSERQNRSDAYAAVILLERYF 212
Cdd:COG0816  84 -AGRFGLPVELVDERLTTVEAERALIEAGVSRKKRKGVIDQIAAVIILQSYL 134
RuvX pfam03652
Holliday junction resolvase; The central intermediate formed during mitotic and meiotic ...
 84-214 6.51e-19

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: 79.86  E-value: 6.51e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79317769    84 LGVDLGLSRTGIAIS--KGYTVKPLTVL--KSRGQKLEtRLLEIAEEEEADEFIIGLPRSSDGKETIQSNKIRSVAGRLA 159
Cdd:pfam03652   4 LGLDFGTKRIGVAVSdpLGITASPLETIprKNGEADLA-ELKELIKEWQPDAIVVGLPLNMDGSEGERTERVRKFARRLK 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 79317769   160 iqaAERGWRVYVFDEHGTTSEASDRMIVMGLSKSERQNRSDAYAAVILLERYFST 214
Cdd:pfam03652  83 ---KRFGLPVELVDERLSTVEAERRLIEAGVSRKKRKEVVDSIAAVIILQSYLDS 134
PRK00109 PRK00109
Holliday junction resolvase RuvX;
84-212 6.90e-13

Holliday junction resolvase RuvX;


Pssm-ID: 234639  Cd Length: 138  Bit Score: 64.02  E-value: 6.90e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79317769   84 LGVDLGLSRTGIAIS--KGYTVKPLTVLKSRGQKLE-TRLLEIAEEEEADEFIIGLPRSSDGKETIQSNKIR----SVAG 156
Cdd:PRK00109   7 LGLDVGTKRIGVAVSdpLGGTAQPLETIKRNNGTPDwDRLEKLIKEWQPDGLVVGLPLNMDGTEGPRTERARkfanRLEG 86

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 79317769  157 RLAIQaaergwrVYVFDEHGTTSEASDRMIVMGLSKSERQNRSDAYAAVILLERYF 212
Cdd:PRK00109  87 RFGLP-------VVLVDERLSTVEAERALADVGSRKKLRKGVIDSLAAVIILQSYL 135
RNAse_H_YqgF TIGR00250
putative transcription antitermination factor YqgF; This protein family, which exhibits an ...
 84-212 1.99e-09

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: 54.45  E-value: 1.99e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79317769    84 LGVDLGLSRTGIAISK--GYTVKPLTVLK-SRGQKLETRLLEIAEEEEADEFIIGLPRSSDGKETIQSNKIRSVAGRLAI 160
Cdd:TIGR00250   1 LGLDFGTKSIGVAGQDitGWTAQGIPTIKaQDGEPDWSRIEELLKEWTPDKIVVGLPLNMDGTEGPLTERAQKFANRLEG 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 79317769   161 QAaerGWRVYVFDEHGTTSEASDRMIVMGLSKSERQNRSDAYAAVILLERYF 212
Cdd:TIGR00250  81 RF---GVPVVLWDERLSTVEAESGLFARGGFRALRKGKIDKAAAVIILQSYL 129
YqgFc smart00732
Likely ribonuclease with RNase H fold; YqgF proteins are likely to function as an alternative ...
 84-181 2.10e-03

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: 36.78  E-value: 2.10e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79317769     84 LGVDLGLSRTGIAIS--KGYTVKPLTVLK-SRGQKLETRLLEIAEEEEADEFIIGLPRSSDGKETIQSNKI--RSVAGRL 158
Cdd:smart00732   4 LGLDPGRKGIGVAVVdeTGKLADPLEVIPrTNKEADAARLKKLIKKYQPDLIVIGLPLNMNGTASRETEEAfaELLKERF 83

                           90       100
                   ....*....|....*....|...
gi 79317769    159 AIQaaergwrVYVFDEHGTTSEA 181
Cdd:smart00732  84 NLP-------VVLVDERLATVYA 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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