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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] (141)
  Mainly parallel beta sheets (beta-alpha-beta units)
Fold:   Restriction endonuclease-like [ 52979] (3)
  core: 3 layers, a/b/a; mixed beta-sheet of 5 strands, order 12345; strands 2 &, in some families, 5 are antiparallel to the rest
Superfamily:   Restriction endonuclease-like [ 52980] (31)
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)
  Pfam 01870
  XPF/Rad1/Mus81 nuclease [ 89716] (3)
  Restriction endonuclease MspI [ 110624]
  Exodeoxyribonuclease V beta chain (RecB), C-terminal domain [ 117619]
  related to the RecC domain
  Exodeoxyribonuclease V beta chain (RecC), C-terminal domain [ 117622]
  related to the RecB domain
  Hypothetical protein VC1899 [ 117625]
  contains 2 extra N-terminal domains; d1: [alpha/beta; 3 layers: a/b/a; mixed beta-sheet of 7 strands, order 3214567; strand 6 is antiparallel to the rest; topological similarity to the Formyltransferase fold (scop_cf 53327)]; d2: [distorted "winged helix" fold (scop_sf 46785)]
  Hypothetical protein TT1808 (TTHA1514) [ 117628]
  Pfam 05685; DUF820
  RecU-like [ 117631]
  Pfam 03838
  Restriction endonuclease EcoO109IR [ 117635]
  MRR-like [ 117638]
  Pfam 04471
  PA4535-like [ 142449]
  contains the PD motif at the beginning of strand 2 and putative catalytic glutamate in strand 3, whereas the putative catalytic lysine is migrated to an alpha-helix

 Superfamily statistics
Genomes (1,218) UniProt 15.0 PDB chains (SCOP 1.73)
Domains 6,751 8,503 57
Proteins 6,729 8,472 57

 Functional annotation
General category Information
Detailed category DNA replication/repair

Function annotation of SCOP domain superfamilies
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 ]

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 37 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 37 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 · Internal database links ]
Please cite: Gough, J., Karplus, K., Hughey, R. and Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a Library of Hidden Markov Models that Represent all Proteins of Known Structure." J. Mol. Biol., 313(4), 903-919.

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© Copyright 2001-2010 The Medical Research Council and the SUPERFAMILY authors; Derek Wilson, Martin Madera and Julian Gough.