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Ribonuclease H-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Ribonuclease H-like motif [ 53066] (7)
Superfamily:   Ribonuclease H-like [ 53098] (14)
Families:   Ribonuclease H [ 53099] (4)
  Retroviral integrase, catalytic domain [ 53107]
  mu transposase, core domain [ 53112]
  Transposase inhibitor (Tn5 transposase) [ 53115]
  DnaQ-like 3'-5' exonuclease [ 53118] (15)
  RuvC resolvase [ 53134]
  Mitochondrial resolvase ydc2 catalytic domain [ 69533]
  Putative Holliday junction resolvase RuvX [ 102485] (3)
  CAF1-like ribonuclease [ 102492] (2)
  PIWI domain [ 110640] (3)
  TM1739-like [ 142505]
  Hermes transposase-like [ 142508]
  Tex RuvX-like domain-like [ 159635]
  Prp8 beta-finger domain-like [ 159638]

Superfamily statistics
Genomes (3,259) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 132,337 0 182
Proteins 128,491 0 182

Functional annotation
General category Metabolism
Detailed category Nucleotide metabolism and transport

Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Nucleotidyltransferases0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)1Least InformativeInherited
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0Moderately InformativeDirect
Enzyme Commission (EC)DNA-directed DNA polymerase0Moderately InformativeDirect
Enzyme Commission (EC)Aspartic endopeptidases0InformativeDirect
Enzyme Commission (EC)RNA-directed DNA polymerase0InformativeDirect
Enzyme Commission (EC)Exoribonuclease H0.0000000008901InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0.000000001817InformativeDirect
Enzyme Commission (EC)Ribonuclease H0Highly InformativeDirect
Enzyme Commission (EC)Exodeoxyribonuclease III0.000005258Highly InformativeDirect

Document: EC annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the head0.01362Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.1213Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.1673Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin morphology0.04796Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.2239Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.5697Moderately InformativeInherited
Phenotypic Abnormality (PA)Vascular skin abnormality0.00909InformativeInherited
Phenotypic Abnormality (PA)Telangiectasia0.00001123Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the nasal dorsum0.03905Highly InformativeInherited

Document: HP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.9499Least InformativeInherited
Worm Phenotype (WP)RNA expression variant0.000000003294InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.00000009143InformativeDirect
Worm Phenotype (WP)RNAi response variant0.0000000000035Highly InformativeDirect
Worm Phenotype (WP)transgene silencing variant0.7949Highly InformativeInherited

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details) Document: YP annotation of SCOP domains

Fly Anatomy (FA)

(show details) Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA 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)trunk0.0003837Least InformativeDirect
Xenopus ANatomical entity (XAN)cavitated compound organ0.02312Least InformativeInherited
Xenopus ANatomical entity (XAN)testis0.0000023Moderately InformativeDirect

Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Transferring phosphorus-containing groups0Least InformativeDirect
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Nucleotidyltransferases0Moderately InformativeDirect
Enzyme Commission (EC)Acting on peptide bonds (peptidases)1Moderately InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides1Moderately InformativeInherited
Enzyme Commission (EC)DNA-directed DNA polymerase0InformativeDirect
Enzyme Commission (EC)Exoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)Endoribonucleases producing 5'-phosphomonoesters0InformativeDirect
Enzyme Commission (EC)In phosphorus-containing anhydrides1InformativeInherited
Enzyme Commission (EC)RNA-directed DNA polymerase0Highly InformativeDirect
Enzyme Commission (EC)HIV-1 retropepsin0Highly InformativeDirect
Enzyme Commission (EC)Exoribonuclease H0.00000000106Highly InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0.000000008654Highly InformativeDirect
Enzyme Commission (EC)HIV-2 retropepsin0.00001989Highly InformativeDirect
Enzyme Commission (EC)Exodeoxyribonucleases producing 5'-phosphomonoesters1Highly 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 processHost-virus interaction0Moderately InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processDNA replication0InformativeDirect
Biological processRibosome biogenesis0InformativeDirect
Biological processVirus entry into host cell0InformativeDirect
Biological processEukaryotic host gene expression shutoff by virus0InformativeDirect
Biological processTranslation regulation0.000000000001176InformativeDirect
Biological processmRNA processing0.00000003478InformativeDirect
Biological processMeiosis0.0000000726InformativeDirect
Biological processDNA repair0.0001068InformativeDirect
Biological processViral immunoevasion1InformativeInherited
Biological processDNA integration0Highly InformativeDirect
Biological processRNA-mediated gene silencing0Highly InformativeDirect
Biological processModulation of host cell apoptosis by virus0Highly InformativeDirect
Biological processViral penetration into host nucleus0Highly InformativeDirect
Biological processViral genome integration0Highly InformativeDirect
Biological processViral release from host cell0Highly InformativeDirect
Biological processEukaryotic host translation shutoff by virus0Highly InformativeDirect
Biological processNonsense-mediated mRNA decay0.000005737Highly InformativeDirect
Biological processIntron homing0.00001366Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Cellular componentMembrane1Least InformativeInherited
Cellular componentVirion0Moderately InformativeDirect
Cellular componentMitochondrion1Moderately InformativeInherited
Cellular componentCapsid protein0InformativeDirect
Cellular componentHost cytoplasm0InformativeDirect
Cellular componentHost membrane0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Cellular componentHost endosome0Highly InformativeDirect
Cellular componentViral matrix protein0.0000000005265Highly InformativeDirect
Coding sequence diversityRibosomal frameshifting0Moderately InformativeDirect
Coding sequence diversityRNA suppression of termination0.000000000003199InformativeDirect
DiseaseAIDS0Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainSH2 domain0.000001881InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionManganese0Moderately InformativeDirect
Molecular functionLipid-binding0.0000000001862Moderately InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationMultifunctional enzyme0Moderately InformativeDirect
Post-translational modificationNuclease0Moderately InformativeDirect
Post-translational modificationNucleotidyltransferase0Moderately InformativeDirect
Post-translational modificationProtease1Moderately InformativeInherited
Post-translational modificationAspartyl protease0Highly InformativeDirect
Post-translational modificationDNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationViral nucleoprotein0Highly InformativeDirect
Post-translational modificationRNA-directed DNA polymerase0Highly InformativeDirect
Post-translational modificationMyristate0InformativeDirect
Post-translational modificationAutocatalytic cleavage0.9833InformativeInherited
Post-translational modificationProtein splicing0.0000000001884Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR012337 SSF53098 Protein matches

The catalytic domain of several polynucleotidyl transferases share a similar structure, consisting of a 3-layer alpha/beta/alpha fold that contains mixed beta sheets, suggesting that they share a similar mechanism of catalysis. Polynucleotidyl transferases containing this domain include ribonuclease H class I (RNase HI) and class II (RNase HII), HIV RNase (reverse transcriptase domain), retroviral integrase (catalytic domain), Mu transposase (core domain), transposase inhibitor Tn5 (containing additional all-alpha subdomains), DnaQ-like 3-5 exonucleases (exonuclease domains), RuvC resolvase, and mitochondrial resolvase ydc2 (catalytic domain) [PubMed15299518, PubMed8696976, PubMed12823554].

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) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · 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 58 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 Ribonuclease H-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 58 hidden Markov models representing the Ribonuclease H-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) · Human Phenotype (HP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]