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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) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000000000006667 Least Informative Direct
Biological Process (BP) response to stimulus 0.000000001021 Least Informative Direct
Biological Process (BP) primary metabolic process 0.0001112 Least Informative Direct
Biological Process (BP) biosynthetic process 0.8477 Least Informative Inherited
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.06358 Least Informative Inherited
Biological Process (BP) cellular response to stress 0 Moderately Informative Direct
Biological Process (BP) organelle organization 0.00004652 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.0009087 Moderately Informative Direct
Biological Process (BP) gene expression 1 Moderately Informative Inherited
Biological Process (BP) organic cyclic compound biosynthetic process 0.9319 Moderately Informative Inherited
Biological Process (BP) RNA metabolic process 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.5929 Moderately Informative Inherited
Biological Process (BP) purine-containing compound metabolic process 0.1368 Moderately Informative Inherited
Biological Process (BP) carbohydrate derivative metabolic process 0.8247 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.4415 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.7813 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.03745 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.02619 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.5865 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.6945 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.3284 Moderately Informative Inherited
Biological Process (BP) cell communication 0.6834 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.6265 Moderately Informative Inherited
Biological Process (BP) reproduction 0.003062 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.09865 Moderately Informative Inherited
Biological Process (BP) heterocycle biosynthetic process 0.7856 Moderately Informative Inherited
Biological Process (BP) aromatic compound biosynthetic process 0.6834 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule biosynthetic process 0.06788 Moderately Informative Inherited
Biological Process (BP) nucleoside phosphate metabolic process 0.01837 Moderately Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0.07661 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.00000000000001597 Informative Direct
Biological Process (BP) response to extracellular stimulus 0.0000000004586 Informative Direct
Biological Process (BP) regulation of organelle organization 0.00000006677 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.0000003588 Informative Direct
Biological Process (BP) response to radiation 0.0000003818 Informative Direct
Biological Process (BP) cell cycle process 0.0000129 Informative Direct
Biological Process (BP) ATP metabolic process 0.0001694 Informative Direct
Biological Process (BP) single organism reproductive process 0.0002021 Informative Direct
Biological Process (BP) transcription, DNA-templated 0.0004518 Informative Direct
Biological Process (BP) organelle localization 0.001477 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.231 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.1561 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.492 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.5399 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.4071 Informative Inherited
Biological Process (BP) regulation of protein modification process 0.2021 Informative Inherited
Biological Process (BP) mitotic cell cycle 1 Informative Inherited
Biological Process (BP) phosphorylation 0.1699 Informative Inherited
Biological Process (BP) chromosome organization 0.02502 Informative Inherited
Biological Process (BP) nuclear division 0.0000000000005804 Highly Informative Direct
Biological Process (BP) negative regulation of homeostatic process 0.000000003553 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.000000003742 Highly Informative Direct
Biological Process (BP) response to UV 0.000000005025 Highly Informative Direct
Biological Process (BP) nuclear chromosome segregation 0.000000662 Highly Informative Direct
Biological Process (BP) nucleic acid phosphodiester bond hydrolysis 0.0000008549 Highly Informative Direct
Biological Process (BP) DNA recombination 0.000001396 Highly Informative Direct
Biological Process (BP) cellular response to extracellular stimulus 0.000002941 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.000002985 Highly Informative Direct
Biological Process (BP) mitochondrial gene expression 0.0001015 Highly Informative Direct
Biological Process (BP) meiotic cell cycle 0.0001718 Highly Informative Direct
Biological Process (BP) establishment of organelle localization 0.0002433 Highly Informative Direct
Biological Process (BP) positive regulation of transcription from RNA polymerase II promoter 0.06471 Highly Informative Inherited
Molecular Function (MF) hydrolase activity 0.00006864 Least Informative Direct
Molecular Function (MF) binding 0.3103 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.000001211 Moderately Informative Direct
Molecular Function (MF) molecular function regulator 0.03511 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.005828 Moderately Informative Inherited
Molecular Function (MF) nuclease activity 0 Informative Direct
Molecular Function (MF) ligase activity 0.002213 Informative Inherited
Molecular Function (MF) DNA binding 0.01296 Informative Inherited
Molecular Function (MF) deoxyribonuclease activity 0 Highly Informative Direct
Molecular Function (MF) single-stranded DNA binding 0.00000007607 Highly Informative Direct
Molecular Function (MF) chromatin binding 0.0005829 Highly Informative Direct
Cellular Component (CC) intracellular organelle part 0.00009461 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.06423 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.001793 Least Informative Inherited
Cellular Component (CC) protein complex 0.01006 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.00000005714 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.0000001025 Moderately Informative Direct
Cellular Component (CC) chromosome 0.0001003 Informative Direct
Cellular Component (CC) nuclear chromosome part 0.02135 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDNA damage0Moderately InformativeDirect
Biological processDNA repair0InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processSOS response0Highly InformativeDirect
Biological processDNA excision0Highly InformativeDirect
Cellular componentMitochondrion1Moderately InformativeInherited
DomainSH2 domain0.000000009899InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionNucleotide-binding0.1462Least 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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]