SUPERFAMILY 1.75 HMM library and genome assignments server

RuvA domain 2-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   SAM domain-like [ 47768] (16)
Superfamily:   RuvA domain 2-like [ 47781] (7)
Families:   DNA helicase RuvA subunit, middle domain [ 47782]
  Excinuclease UvrC C-terminal domain [ 81795]
  NAD+-dependent DNA ligase, domain 3 [ 47786]
  Topoisomerase V repeat domain [ 140626]
  Hef domain-like [ 140629] (3)
  Tex HhH-containing domain-like [ 158531]
  ComEA-like [ 158534] (2)


Superfamily statistics
Genomes (3,202) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 20,282 117,169 24
Proteins 17,688 101,607 19


Functional annotation
General category Information
Detailed category DNA replication/repair

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0000000000002211 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.00000000001343 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.000009782 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) response to stimulus 0.0002737 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000000000000003707 Least Informative Direct
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.6485 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.0211 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.08596 Least Informative Inherited
Biological Process (BP) biosynthetic process 0.5847 Least Informative Inherited
Biological Process (BP) cellular response to stress 0.000000000000003707 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.0007072 Moderately Informative Direct
Biological Process (BP) single-organism organelle organization 0.00003834 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.009492 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 0.9921 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.871 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.9666 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.3308 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.2921 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.1729 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.009066 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.06065 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.4521 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.3222 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.3141 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.05938 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.5003 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.9621 Moderately Informative Inherited
Biological Process (BP) organophosphate metabolic process 0.7856 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing small molecule metabolic process 0.2958 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.8586 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.8505 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.02583 Moderately Informative Inherited
Biological Process (BP) DNA repair 0 Informative Direct
Biological Process (BP) transcription, DNA-templated 0.00007833 Informative Direct
Biological Process (BP) regulation of organelle organization 0.0000001067 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 0.000006823 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.00000003153 Informative Direct
Biological Process (BP) cell division 0.0002061 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.0000007875 Informative Direct
Biological Process (BP) organelle fission 0.001194 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.005415 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.1975 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.4308 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.3954 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.3263 Informative Inherited
Biological Process (BP) positive regulation of RNA metabolic process 0.2748 Informative Inherited
Biological Process (BP) response to light stimulus 0.2885 Informative Inherited
Biological Process (BP) cell cycle process 0.001136 Informative Inherited
Biological Process (BP) mitochondrion organization 0.04779 Informative Inherited
Biological Process (BP) nucleoside monophosphate metabolic process 0.003037 Informative Inherited
Biological Process (BP) nucleoside triphosphate metabolic process 0.009778 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.01958 Informative Inherited
Biological Process (BP) phosphorylation 0.1798 Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0.0153 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.01354 Informative Inherited
Biological Process (BP) nuclear division 0.0000009764 Highly Informative Direct
Biological Process (BP) oxidative phosphorylation 0.00000005119 Highly Informative Direct
Biological Process (BP) DNA catabolic process 0.00000000000861 Highly Informative Direct
Biological Process (BP) DNA recombination 0.000003944 Highly Informative Direct
Biological Process (BP) chromosome segregation 0.00002991 Highly Informative Direct
Biological Process (BP) response to UV 0.0000001182 Highly Informative Direct
Biological Process (BP) negative regulation of homeostatic process 0.0000000002751 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.0000000002208 Highly Informative Direct
Biological Process (BP) meiotic cell cycle 0.00001028 Highly Informative Direct
Biological Process (BP) negative regulation of chromosome organization 0.00000001778 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-templated 0.2462 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.000001616 Least Informative Direct
Molecular Function (MF) binding 0.3083 Least Informative Inherited
Molecular Function (MF) nucleic acid binding 0.0005159 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.000002042 Moderately Informative Direct
Molecular Function (MF) enzyme regulator activity 0.01118 Moderately Informative Inherited
Molecular Function (MF) chromatin binding 0.0006366 Informative Direct
Molecular Function (MF) nuclease activity 0 Informative Direct
Molecular Function (MF) DNA binding 0.01273 Informative Inherited
Molecular Function (MF) structure-specific DNA binding 0.0001059 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.000002788 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.000002715 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.04176 Least Informative Inherited
Cellular Component (CC) protein complex 0.8638 Least Informative Inherited
Cellular Component (CC) nuclear part 0.00000006596 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 0.00001347 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.06304 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.0005313 Informative Direct
Cellular Component (CC) mitochondrial matrix 0.05258 Informative Inherited
Cellular Component (CC) nuclear chromosome part 0.01453 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Ligases0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides0Least InformativeDirect
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0Moderately InformativeDirect
Enzyme Commission (EC)Ligases that form phosphoric-ester bonds1InformativeInherited
Enzyme Commission (EC)DNA ligase (NAD(+))0Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)immune system disease0.00653Least InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.000299Moderately InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of head and neck0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system physiology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the skull0Moderately InformativeDirect
Phenotypic Abnormality (PA)Growth abnormality0Moderately InformativeDirect
Phenotypic Abnormality (PA)Generalized abnormality of skin0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skull size0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the ear0InformativeDirect
Phenotypic Abnormality (PA)Growth delay0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of body height0Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)premature death0InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)male organism0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)flower0Least InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorous-containing groups1Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)Ligases0Moderately InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases1Moderately InformativeInherited
Enzyme Commission (EC)DNA helicase0InformativeDirect
Enzyme Commission (EC)Ligases that form phosphoric-ester bonds1Highly InformativeInherited

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processDNA excision0Highly InformativeDirect
Biological processSOS response0Highly InformativeDirect
Cellular componentMitochondrion1Moderately InformativeInherited
DomainSH2 domain0.000000008041InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionNucleotide-binding0.000000000009419Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationLigase0Moderately InformativeDirect
Post-translational modificationHelicase0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR010994 SSF47781 Protein matches
Abstract

In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure [PubMed12408833]. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. Domain 2 has a SAM (sterile alpha motif)-like alpha bundle fold that occurs as a duplication containing two helix-hairpin-helix (HhH) motifs.

The C-terminal domain (CTD) of the excision repair protein UvrC shows structural similarity to RuvA domain 2. The CTD of UvrC is essential for 5' incision in the prokaryotic nucleotide excision repair process, and acts to mediate structure-specific binding to single-stranded-double-stranded junction DNA [PubMed12426397].

Domain 3 of NAD+-dependent DNA ligase consists of a duplication of two RuvA-like domains (four HhH motifs), and also contains a zinc-finger subdomain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD+ as a cofactor [PubMed10698952].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 17 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a RuvA domain 2-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 17 hidden Markov models representing the RuvA domain 2-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]