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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 (3,210) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 20,351 157,351 24
Proteins 17,736 136,802 19


Functional annotation
General category Information
Detailed category DNA replication/repair

Document:
Function annotation of SCOP domain superfamilies

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 disease0.00002243Moderately 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 the head0Least 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 system0.134Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the eye0.2191Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the vertebral column0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the skull0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormal joint morphology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Growth abnormality0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the lower limb0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the upper limb0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skin morphology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Neurodevelopmental abnormality0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.01898Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.02524Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal globe morphology0.1198Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the orbital region0.2854Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the forehead0InformativeDirect
Phenotypic Abnormality (PA)Global developmental delay0InformativeDirect
Phenotypic Abnormality (PA)Joint dislocation0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of pelvic girdle bone morphology0InformativeDirect
Phenotypic Abnormality (PA)Scoliosis0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the calvaria0InformativeDirect
Phenotypic Abnormality (PA)Short stature0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the synovia0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of phalanx of finger0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of long bone morphology0InformativeDirect
Phenotypic Abnormality (PA)Abnormal ear morphology0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of lower limb joint0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.001018InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.002444InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the spinal cord0.003057InformativeInherited
Phenotypic Abnormality (PA)Abnormal eyelid morphology0.01841InformativeInherited
Phenotypic Abnormality (PA)Abnormal morphology of bones of the lower limbs0.02185InformativeInherited
Phenotypic Abnormality (PA)Aplasia/hypoplasia of the extremities0.04281InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the radius0Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal size of the palpebral fissures0.00009662Highly InformativeDirect
Phenotypic Abnormality (PA)Microphthalmia0.0001275Highly InformativeDirect
Phenotypic Abnormality (PA)Hypogonadism0.0009924Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of calvarial morphology0.6173Highly InformativeInherited

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 phenotype0.04912Least InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.0006152Moderately 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)cavitated compound organ0Least 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

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 · 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) ]

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 · 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) · Internal database links ]