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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 132,337 626,221 182
Proteins 128,491 598,729 182


Functional annotation
General category Metabolism
Detailed category Nucleotide metabolism and transport

Document:
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 head0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.002148Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.05881Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.06206Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.3168Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.0008486Moderately InformativeDirect
Phenotypic Abnormality (PA)Neoplasm0.023Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of connective tissue0.03487Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal peripheral nervous system morphology0.1862Moderately InformativeInherited
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0.4193Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.5018Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal skull morphology0.5084Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of forebrain morphology0.5445Moderately InformativeInherited
Phenotypic Abnormality (PA)Lipodystrophy0.0001754InformativeDirect
Phenotypic Abnormality (PA)Abnormal glucose homeostasis0.007781InformativeInherited
Phenotypic Abnormality (PA)Abnormal breast morphology0.01201InformativeInherited
Phenotypic Abnormality (PA)Microcephaly0.03448InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.2171InformativeInherited
Phenotypic Abnormality (PA)Peripheral neuropathy0.3618InformativeInherited
Phenotypic Abnormality (PA)Glucose intolerance0.00001515Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the voice0.0004188Highly InformativeDirect
Phenotypic Abnormality (PA)Breast carcinoma0.0004704Highly InformativeDirect
Phenotypic Abnormality (PA)Postnatal microcephaly0.03046Highly 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 variant0.9261Least InformativeInherited
Worm Phenotype (WP)RNA expression variant0.000000002036InformativeDirect
Worm Phenotype (WP)maintenance of gene silencing variant0.00000009159InformativeDirect
Worm Phenotype (WP)RNAi response variant0.000000000003149Highly InformativeDirect
Worm Phenotype (WP)transgene silencing variant0.7909Highly 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)trunk0.0004489Least InformativeDirect
Xenopus ANatomical entity (XAN)cavitated compound organ0.02468Least InformativeInherited
Xenopus ANatomical entity (XAN)anatomical system1Least InformativeInherited
Xenopus ANatomical entity (XAN)testis0.000002395Moderately 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 H0.000000001851Highly InformativeDirect
Enzyme Commission (EC)Retroviral ribonuclease H0.000000009792Highly InformativeDirect
Enzyme Commission (EC)HIV-2 retropepsin0.0000201Highly InformativeDirect
Enzyme Commission (EC)dUTP diphosphatase0.00003469Highly InformativeDirect
Enzyme Commission (EC)Exodeoxyribonucleases producing 5'-phosphomonoesters1Highly InformativeInherited

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR012337 SSF53098 Protein matches
Abstract

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) ]

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 88 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 88 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) · Internal database links ]