SUPERFAMILY 1.75 HMM library and genome assignments server


XRCC4, N-terminal domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   XRCC4, N-terminal domain [ 50808]
Superfamily:   XRCC4, N-terminal domain [ 50809]
Families:   XRCC4, N-terminal domain [ 50810]


Superfamily statistics
Genomes (85) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 109 0 2
Proteins 108 0 2


Functional annotation
General category Information
Detailed category DNA replication/repair

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 1.638e-05 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 4.546e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0001205 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0003604 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 1.475e-05 Least Informative Direct
Biological Process (BP) response to stimulus 3.551e-05 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 2.532e-05 Least Informative Direct
Biological Process (BP) cellular response to stress 0.0009673 Moderately Informative Direct
Biological Process (BP) DNA metabolic process 9.099e-09 Informative Direct
Biological Process (BP) response to DNA damage stimulus 1.582e-09 Informative Direct
Biological Process (BP) double-strand break repair 4.372e-13 Highly Informative Direct
Cellular Component (CC) protein complex 1.113e-05 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.0001085 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.002921 Least Informative Inherited
Cellular Component (CC) nuclear part 1.65e-06 Moderately Informative Direct

Document: GO annotation of SCOP domains

InterPro annotation
Cross references IPR009089 SSF50809 Protein matches
Abstract

XRCC4 is essential for non-homologous DNA end joining (NHDJ) in eukaryotes, which is required for double-strand break repair, and V(D)J recombination in immunoglobulin and T-cell receptor genes. XRCC4 forms a complex with DNA ligase IV, and acts as a regulatory element required for the stability and activity of the ligase. XRCC4 forms an elongated dumb-bell-like tetramer consisting of a C-terminal stalk that interacts with DNA ligase IV and an N-terminal globular head. The N-terminal head domain consists of a beta sandwich and a helix-turn-helix (HTH) motif, which may be involved in DNA binding [PubMed11080143, PubMed11702069].


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 · Gene Ontology (high-coverage) ]

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 1 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 XRCC4, N-terminal domain 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 1 hidden Markov models representing the XRCC4, N-terminal domain 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 · Gene Ontology (high-coverage) · Internal database links ]