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Restriction endonuclease-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Restriction endonuclease-like [ 52979] (4)
Superfamily:   Restriction endonuclease-like [ 52980] (33)
Families:   Restriction endonuclease EcoRI [ 52981]
  Restriction endonuclease EcoRV [ 52984]
  Restriction endonuclease BamHI [ 52987]
  Restriction endonuclease BglI [ 52990]
  Restriction endonuclease BglII [ 52993]
  Restriction endonuclease BstyI [ 102471]
  Restriction endonuclease PvuII [ 52996]
  Cfr10I/Bse634I [ 52999] (2)
  Restriction endonuclease MunI [ 53002]
  Restriction endonuclease NaeI [ 53005]
  Restriction endonuclease NgoIV [ 53008]
  Restriction endonuclease BsobI [ 53011]
  Restriction endonuclease HincII [ 69525]
  Restriction endonuclease FokI, C-terminal (catalytic) domain [ 53014]
  Type II restriction endonuclease catalytic domain [ 102474]
  lambda exonuclease [ 53017]
  DNA mismatch repair protein MutH from [ 53020]
  Very short patch repair (VSR) endonuclease [ 53023]
  TnsA endonuclease, N-terminal domain [ 53026]
  Endonuclease I (Holliday junction resolvase) [ 53029]
  Hjc-like [ 64080] (2)
  XPF/Rad1/Mus81 nuclease [ 89716] (3)
  Restriction endonuclease MspI [ 110624]
  Exodeoxyribonuclease V beta chain (RecB), C-terminal domain [ 117619]
  Exodeoxyribonuclease V beta chain (RecC), C-terminal domain [ 117622]
  Hypothetical protein VC1899 [ 117625]
  Hypothetical protein TT1808 (TTHA1514) [ 117628]
  RecU-like [ 117631]
  Restriction endonuclease EcoO109IR [ 117635]
  MRR-like [ 117638]
  PA4535-like [ 142449]
  XisH-like [ 159601]
  YaeQ-like [ 159605] (2)


Superfamily statistics
Genomes (3,197) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 19,809 155,302 63
Proteins 19,730 154,497 63


Functional annotation
General category Information
Detailed category DNA replication/repair

Document:
Function annotation of SCOP domain superfamilies

Enzyme Commission (EC)

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EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on acid anhydrides0Least InformativeDirect
Enzyme Commission (EC)Acting on ester bonds1Least InformativeInherited
Enzyme Commission (EC)Acting on acid anhydrides; involved in cellular an0Moderately InformativeDirect
Enzyme Commission (EC)Endodeoxyribonucleases producing 5'-phosphomonoest0Highly InformativeDirect

Document: EC annotation of SCOP domains

Disease Ontology (DO)

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DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)hematopoietic system disease0.0002403Moderately InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

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HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the head0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the eye0Least 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 the digestive system0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of limbs0.08527Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the vertebral column0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the skull0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the cerebrum0Moderately InformativeDirect
Phenotypic Abnormality (PA)Aplasia/Hypoplasia involving the central nervous system0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of immune system physiology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormal eye physiology0Moderately InformativeDirect
Phenotypic Abnormality (PA)Neurodevelopmental abnormality0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of movement0Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of limb bone morphology0.03353Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper limb0.03517Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower limb0.03999Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal globe morphology0.1198Moderately InformativeInherited
Phenotypic Abnormality (PA)Growth abnormality0.1366Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.177Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the orbital region0.2854Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0InformativeDirect
Phenotypic Abnormality (PA)Microcephaly0InformativeDirect
Phenotypic Abnormality (PA)Abnormal reflex0InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the synovia0.0003618InformativeDirect
Phenotypic Abnormality (PA)Joint dislocation0.000692InformativeDirect
Phenotypic Abnormality (PA)Abnormality of pelvic girdle bone morphology0.002131InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lower limb joint0.002336InformativeInherited
Phenotypic Abnormality (PA)Abnormal eyelid morphology0.01841InformativeInherited
Phenotypic Abnormality (PA)Hypogonadism0Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal size of the palpebral fissures0.00009662Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the radius0.0001155Highly InformativeDirect
Phenotypic Abnormality (PA)Microphthalmia0.0001275Highly InformativeDirect
Phenotypic Abnormality (PA)Cranial nerve paralysis0.000249Highly InformativeDirect
Phenotypic Abnormality (PA)Intrauterine growth retardation0.0007542Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0Least InformativeDirect
Mammalian Phenotype (MP)neoplasm0.002007Moderately InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

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WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0Least InformativeDirect
Worm Phenotype (WP)general pace of development variant0Least InformativeDirect
Worm Phenotype (WP)larval lethal0Least InformativeDirect
Worm Phenotype (WP)retarded heterochronic variations0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0Least InformativeDirect
Worm Phenotype (WP)organism environmental stimulus response variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)larval growth variant0Least InformativeDirect
Worm Phenotype (WP)cell homeostasis metabolism variant0Moderately InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect
Yeast Phenotype (YP)radiation resistance0Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)chemical sensitive0Highly InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

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XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)trunk0Least InformativeDirect
Xenopus ANatomical entity (XAN)cavitated compound organ0Least InformativeDirect
Xenopus ANatomical entity (XAN)testis0Moderately InformativeDirect
Xenopus ANatomical entity (XAN)germ line cell0Moderately InformativeDirect
Xenopus DEvelopment stage (XDE)unfertilized egg stage0Highly 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)guard cell0Least InformativeDirect
Plant ANatomical entity (PAN)flower0Least InformativeDirect
Plant ANatomical entity (PAN)shoot axis0Least InformativeDirect
Plant ANatomical entity (PAN)leaf0Least 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)Acting on acid anhydrides0Moderately InformativeDirect
Enzyme Commission (EC)DNA helicase0InformativeDirect
Enzyme Commission (EC)Endodeoxyribonucleases producing 5'-phosphomonoesters0Highly InformativeDirect
Enzyme Commission (EC)Exodeoxyribonucleases producing 5'-phosphomonoesters0.000000002095Highly InformativeDirect

Document: EC annotation of SCOP domains

InterPro annotation
Cross references IPR011335 SSF52980 Protein matches
Abstract

This entry represents the core structure found in most type II restriction endonucleases, consisting of a 3-layer alpha/beta/alpha topology with mixed beta-sheets. This core structure can be found in the restriction endonucleases EcoRI, EcoRV, BamHI, BglI, BglII, BstyI, PvuII, MunI, NseI, NgoIV, BsobI, HincII, MspI, FokI (C-terminal), EcoO109IR, as well as in lamba exonuclease, DNA mismatch repair protein MutH, VSR (very short repair) endonucleases, TnsA endonucleases (N-terminal), endonucleases I (Holliday junction resolvase), Hjc-like enzymes, XPF/Rad1/Mus81 nucleases, RecB and RecC exodeoxyribonuclease V (C-terminal), and RecU-like enzymes.


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) · Yeast Phenotype (YP) · Fly Phenotype (FP) · 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 41 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 Restriction endonuclease-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 41 hidden Markov models representing the Restriction endonuclease-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) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · Internal database links ]