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 (3,200) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 20,266 117,169 24
Proteins 17,673 101,607 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) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 1.936e-15 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 9.259e-14 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 8.126e-12 Least Informative Direct
Biological Process (BP) response to stimulus 0.0001912 Least Informative Direct
Biological Process (BP) biosynthetic process 0.6136 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.5555 Least Informative Inherited
Biological Process (BP) regulation of cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.18 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.001569 Least Informative Inherited
Biological Process (BP) cellular response to stress 3.752e-15 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.0003931 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.1246 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.002307 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.01006 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.5901 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.9985 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.04894 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular nitrogen compound biosynthetic process 0.403 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.4238 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.4426 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.6255 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.3351 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.3105 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.06002 Moderately Informative Inherited
Biological Process (BP) gene expression 0.9672 Moderately Informative Inherited
Biological Process (BP) organelle organization 0.16 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 0.904 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 0.8441 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound catabolic process 0.002182 Moderately Informative Inherited
Biological Process (BP) reproduction 0.009512 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) response to DNA damage stimulus 1.809e-09 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 1.153e-08 Informative Direct
Biological Process (BP) regulation of organelle organization 3.73e-08 Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 8.675e-07 Informative Direct
Biological Process (BP) cellular macromolecule catabolic process 5.925e-06 Informative Direct
Biological Process (BP) transcription, DNA-dependent 0.0001096 Informative Direct
Biological Process (BP) cellular process involved in reproduction 0.0002482 Informative Direct
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.1801 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.3067 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.371 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.6643 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.005004 Informative Inherited
Biological Process (BP) response to light stimulus 0.2943 Informative Inherited
Biological Process (BP) mitochondrion organization 0.007819 Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0.01554 Informative Inherited
Biological Process (BP) phosphorylation 0.1146 Informative Inherited
Biological Process (BP) cell cycle process 0.004112 Informative Inherited
Biological Process (BP) DNA catabolic process 1.126e-11 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 8.536e-11 Highly Informative Direct
Biological Process (BP) oxidative phosphorylation 4.94e-08 Highly Informative Direct
Biological Process (BP) response to UV 9.146e-08 Highly Informative Direct
Biological Process (BP) DNA recombination 3.194e-06 Highly Informative Direct
Biological Process (BP) meiosis 1.914e-05 Highly Informative Direct
Biological Process (BP) chromosome segregation 9.47e-05 Highly Informative Direct
Molecular Function (MF) hydrolase activity 1.251e-06 Least Informative Direct
Molecular Function (MF) binding 0.2837 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 1.61e-06 Moderately Informative Direct
Molecular Function (MF) enzyme regulator activity 0.02786 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.001783 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 0 Informative Direct
Molecular Function (MF) DNA binding 3.101e-05 Informative Direct
Molecular Function (MF) chromatin binding 0.0005792 Informative Direct
Molecular Function (MF) structure-specific DNA binding 9.698e-05 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 1.28e-06 Least Informative Direct
Cellular Component (CC) intracellular organelle part 3.141e-06 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.05588 Least Informative Inherited
Cellular Component (CC) protein complex 0.5351 Least Informative Inherited
Cellular Component (CC) nuclear part 4.558e-07 Moderately Informative Direct
Cellular Component (CC) intracellular organelle lumen 8.493e-05 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.06028 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.0007247 Informative Direct
Cellular Component (CC) mitochondrial matrix 0.0368 Informative Inherited
Cellular Component (CC) nuclear chromosome part 0.008724 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 disease0.006542Least InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.0002983Moderately 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 domain8.174e-09InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionNucleotide-binding1.424e-11Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionDNA-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 ]