NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1855776521|ref|WP_174564726|]
View 

crossover junction endodeoxyribonuclease RuvC, partial [Solemya elarraichensis gill symbiont]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RuvC-like super family cl21482
Crossover junction endodeoxyribonuclease RuvC and similar proteins; The RuvC-like family ...
 1-49 2.65e-22

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.


The actual alignment was detected with superfamily member PRK00039:

Pssm-ID: 473878  Cd Length: 164  Bit Score: 82.86  E-value: 2.65e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1855776521   1 VKQAIVGTGGADKAQVTHMVRVLLNLKSEELTEDQADALAIALCHAHTG 49
Cdd:PRK00039  108 VKKAVVGYGRADKEQVQHMVKRLLNLPEIPKPDDAADALAIAICHAHRR 156
 
Name Accession Description Interval E-value
ruvC PRK00039
Holliday junction resolvase; Reviewed
 1-49 2.65e-22

Holliday junction resolvase; Reviewed


Pssm-ID: 234587  Cd Length: 164  Bit Score: 82.86  E-value: 2.65e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1855776521   1 VKQAIVGTGGADKAQVTHMVRVLLNLKSEELTEDQADALAIALCHAHTG 49
Cdd:PRK00039  108 VKKAVVGYGRADKEQVQHMVKRLLNLPEIPKPDDAADALAIAICHAHRR 156
RuvC COG0817
Holliday junction resolvasome RuvABC endonuclease subunit RuvC [Replication, recombination and ...
 1-48 4.08e-22

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


Pssm-ID: 440579  Cd Length: 152  Bit Score: 82.05  E-value: 4.08e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1855776521   1 VKQAIVGTGGADKAQVTHMVRVLLNLKSEELTEDQADALAIALCHAHT 48
Cdd:COG0817   105 VKKAVTGYGRADKEQVQAMVKRLLGLDEIPKPDDAADALAIAICHAHR 152
RuvC cd16962
Crossover junction endodeoxyribonuclease RuvC; Crossover junction endodeoxyribonuclease RuvC ...
 1-48 1.35e-21

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: 80.94  E-value: 1.35e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1855776521   1 VKQAIVGTGGADKAQVTHMVRVLLNLKSEELTEDQADALAIALCHAHT 48
Cdd:cd16962   105 VKQAVTGYGRADKEQVQYMVKRLLGLKEIPKPDDAADALAIALCHAHS 152
RuvC pfam02075
Crossover junction endodeoxyribonuclease RuvC; This entry includes endodeoxyribonucleases ...
 1-45 1.32e-15

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: 65.56  E-value: 1.32e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1855776521   1 VKQAIVGTGGADKAQVTHMVRVLLNLKSEELTEDQADALAIALCH 45
Cdd:pfam02075 104 VKKAVTGNGKAEKEQVQHMVKRLLNLTAKPQPADAADALAVAITH 148
ruvC TIGR00228
crossover junction endodeoxyribonuclease RuvC; Endonuclease that resolves Holliday junction ...
 1-47 1.34e-11

crossover junction endodeoxyribonuclease RuvC; Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129331  Cd Length: 156  Bit Score: 55.32  E-value: 1.34e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1855776521   1 VKQAIVGTGGADKAQVTHMVRVLLNLkSEELTEDQADALAIALCHAH 47
Cdd:TIGR00228 104 VKQTVVGIGSAEKSQVQHMVRRLLKL-PANPQADAADALAIAITHAH 149
 
Name Accession Description Interval E-value
ruvC PRK00039
Holliday junction resolvase; Reviewed
 1-49 2.65e-22

Holliday junction resolvase; Reviewed


Pssm-ID: 234587  Cd Length: 164  Bit Score: 82.86  E-value: 2.65e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1855776521   1 VKQAIVGTGGADKAQVTHMVRVLLNLKSEELTEDQADALAIALCHAHTG 49
Cdd:PRK00039  108 VKKAVVGYGRADKEQVQHMVKRLLNLPEIPKPDDAADALAIAICHAHRR 156
RuvC COG0817
Holliday junction resolvasome RuvABC endonuclease subunit RuvC [Replication, recombination and ...
 1-48 4.08e-22

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


Pssm-ID: 440579  Cd Length: 152  Bit Score: 82.05  E-value: 4.08e-22
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1855776521   1 VKQAIVGTGGADKAQVTHMVRVLLNLKSEELTEDQADALAIALCHAHT 48
Cdd:COG0817   105 VKKAVTGYGRADKEQVQAMVKRLLGLDEIPKPDDAADALAIAICHAHR 152
RuvC cd16962
Crossover junction endodeoxyribonuclease RuvC; Crossover junction endodeoxyribonuclease RuvC ...
 1-48 1.35e-21

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: 80.94  E-value: 1.35e-21
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1855776521   1 VKQAIVGTGGADKAQVTHMVRVLLNLKSEELTEDQADALAIALCHAHT 48
Cdd:cd16962   105 VKQAVTGYGRADKEQVQYMVKRLLGLKEIPKPDDAADALAIALCHAHS 152
RuvC pfam02075
Crossover junction endodeoxyribonuclease RuvC; This entry includes endodeoxyribonucleases ...
 1-45 1.32e-15

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: 65.56  E-value: 1.32e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1855776521   1 VKQAIVGTGGADKAQVTHMVRVLLNLKSEELTEDQADALAIALCH 45
Cdd:pfam02075 104 VKKAVTGNGKAEKEQVQHMVKRLLNLTAKPQPADAADALAVAITH 148
ruvC TIGR00228
crossover junction endodeoxyribonuclease RuvC; Endonuclease that resolves Holliday junction ...
 1-47 1.34e-11

crossover junction endodeoxyribonuclease RuvC; Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129331  Cd Length: 156  Bit Score: 55.32  E-value: 1.34e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1855776521   1 VKQAIVGTGGADKAQVTHMVRVLLNLkSEELTEDQADALAIALCHAH 47
Cdd:TIGR00228 104 VKQTVVGIGSAEKSQVQHMVRRLLKL-PANPQADAADALAIAITHAH 149
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH