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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 (3,208) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 20,315 120,077 24
Proteins 17,710 104,048 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) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0000000000001154 Least Informative Direct
Biological Process (BP) response to stimulus 0.0000000008079 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0001082 Least Informative Direct
Biological Process (BP) biosynthetic process 0.8461 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.06262 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) organelle organization 0.0000554 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.0008491 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.322 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.09725 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.8138 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.7818 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.4398 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.6905 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.935 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.02737 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.5825 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.03738 Moderately Informative Inherited
Biological Process (BP) cell communication 0.6801 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.7032 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.5796 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.5912 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.02014 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.7928 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.06578 Moderately Informative Inherited
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) purine-containing compound metabolic process 0.1392 Moderately Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0.07818 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.003314 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.00000000000004787 Informative Direct
Biological Process (BP) response to extracellular stimulus 0.0000000003613 Informative Direct
Biological Process (BP) regulation of organelle organization 0.00000007114 Informative Direct
Biological Process (BP) response to radiation 0.0000002647 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.0000003499 Informative Direct
Biological Process (BP) cell cycle process 0.00001593 Informative Direct
Biological Process (BP) ATP metabolic process 0.0001993 Informative Direct
Biological Process (BP) single organism reproductive process 0.0002178 Informative Direct
Biological Process (BP) transcription, DNA-templated 0.000516 Informative Direct
Biological Process (BP) organelle localization 0.001263 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.161 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.4093 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.5297 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.4952 Informative Inherited
Biological Process (BP) regulation of transcription, DNA-templated 0.7853 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.2029 Informative Inherited
Biological Process (BP) phosphorylation 0.1772 Informative Inherited
Biological Process (BP) mitotic cell cycle 1 Informative Inherited
Biological Process (BP) chromosome organization 0.02562 Informative Inherited
Biological Process (BP) nuclear division 0.0000000000007493 Highly Informative Direct
Biological Process (BP) negative regulation of homeostatic process 0.000000004497 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.000000005319 Highly Informative Direct
Biological Process (BP) response to UV 0.000000005942 Highly Informative Direct
Biological Process (BP) nuclear chromosome segregation 0.0000007086 Highly Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.0000008542 Highly Informative Direct
Biological Process (BP) DNA recombination 0.000001793 Highly Informative Direct
Biological Process (BP) cellular response to extracellular stimulus 0.000002115 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.00000295 Highly Informative Direct
Biological Process (BP) meiotic cell cycle 0.0001931 Highly Informative Direct
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.2243 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription, DNA-templated 0.2879 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.00008722 Least Informative Direct
Molecular Function (MF) binding 0.2634 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.000001185 Moderately Informative Direct
Molecular Function (MF) molecular function regulator 0.03563 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.005542 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 0 Informative Direct
Molecular Function (MF) ligase activity 0.002193 Informative Inherited
Molecular Function (MF) DNA binding 0.01125 Informative Inherited
Molecular Function (MF) deoxyribonuclease activity 0 Highly Informative Direct
Molecular Function (MF) single-stranded DNA binding 0.0000001001 Highly Informative Direct
Molecular Function (MF) chromatin binding 0.0006772 Highly Informative Direct
Cellular Component (CC) macromolecular complex 0.000003158 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0002277 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.09844 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.001787 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.0000002106 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.0000002149 Moderately Informative Direct
Cellular Component (CC) mitochondrial part 0.1289 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.0001226 Informative Direct
Cellular Component (CC) nuclear chromosome part 0.01946 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)hematopoietic system disease0.00002227Moderately InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Variable expressivity0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the face0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the integument0Least 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 limbs0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.1337Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.1806Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.2258Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the ear0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the vertebral column0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the skull0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the hand0Moderately InformativeDirect
Phenotypic Abnormality (PA)Growth abnormality0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the foot0Moderately InformativeDirect
Phenotypic Abnormality (PA)Aplasia/hypoplasia involving the skeleton0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skin morphology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of digit0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of long bone morphology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of higher mental function0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of lower limb bone0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the urinary system physiology0.0137Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.02035Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.02514Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the anterior segment of the globe0.02606Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.02926Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal genital system morphology0.03122Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the orbital region0.3023Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of body height0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skull size0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the forehead0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the outer ear0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the nasal bridge0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the neck0InformativeDirect
Phenotypic Abnormality (PA)Growth delay0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the femur0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the hip bone0InformativeDirect
Phenotypic Abnormality (PA)Abnormal bone structure0InformativeDirect
Phenotypic Abnormality (PA)Abnormal nasal morphology0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of phalanx of finger0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the curvature of the vertebral column0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the external nose0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of upper limb bone0InformativeDirect
Phenotypic Abnormality (PA)Cognitive impairment0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of globe size0.0001765InformativeDirect
Phenotypic Abnormality (PA)Renal insufficiency0.0005183InformativeDirect
Phenotypic Abnormality (PA)Aplasia/Hypoplasia affecting the eye0.0008572InformativeDirect
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.0009437InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.0009437InformativeDirect
Phenotypic Abnormality (PA)External genital hypoplasia0.002582InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cerebral ventricles0.003415InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the uvea0.003689InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the penis0.004334InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the palpebral fissures0.006113InformativeInherited
Phenotypic Abnormality (PA)Decreased body weight0.01969InformativeInherited
Phenotypic Abnormality (PA)Abnormality of epiphysis morphology0.09307InformativeInherited
Phenotypic Abnormality (PA)Short neck0Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the radius0Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of DNA repair0.00000003564Highly InformativeDirect
Phenotypic Abnormality (PA)Aplasia/Hypoplasia of the iris0.000003725Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the trachea0.00002809Highly InformativeDirect
Phenotypic Abnormality (PA)Spinal dysraphism0.00004548Highly InformativeDirect
Phenotypic Abnormality (PA)Small for gestational age0.0001069Highly InformativeDirect
Phenotypic Abnormality (PA)Blepharophimosis0.0002254Highly InformativeDirect
Phenotypic Abnormality (PA)Hypogonadism0.0002299Highly InformativeDirect
Phenotypic Abnormality (PA)Micropenis0.0002499Highly InformativeDirect
Phenotypic Abnormality (PA)Hydrocephalus0.0004475Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.0492Least InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.0006164Moderately InformativeDirect

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)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 phosphorus-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)Forming 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 domain0.000000009599InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionNucleotide-binding0.1272Least InformativeInherited
Molecular functionManganese0Moderately InformativeDirect
Molecular functionNAD0Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationDNA-binding0Moderately 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 ]