SUPERFAMILY 1.75 HMM library and genome assignments server

Viral DNA-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Ferredoxin-like [ 54861] (59)
Superfamily:   Viral DNA-binding domain [ 54957]
Families:   Viral DNA-binding domain [ 54958] (2)


Superfamily statistics
Genomes (0) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 0 964 12
Proteins 0 964 12


Functional annotation
General category Regulation
Detailed category DNA-binding

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Molecular Function (MF) binding 0.00002116 Least Informative Direct

Document: GO annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processHost-virus interaction0.0000914Moderately InformativeDirect
Biological processDNA replication0InformativeDirect
Cellular componentHost nucleus0InformativeDirect
Developmental stageEarly protein0Least InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009021 SSF54957 Protein matches
Abstract

The Epstein barr virus is a human herpes virus that is associated with several malignancies and diseases. Papillomaviruses infect epithelial cells, and certain strains are associated with tumour formation. The EBNA-1 protein of Epstein barr virus and the E2 protein of papillomavirus both function to activate viral DNA replication. Despite a lack of sequence similarity between these two proteins, the core DNA-binding domain of the EBNA-1 protein shows structural homology to the entire DNA binding and dimerisation domain of the E2 protein. X-ray crystallography reveals the E2 and EBNA1 core DNA-binding domains to be comprised of an eight-stranded beta-barrel, flanked on two sides by two alpha helices [PubMed7553871, PubMed10587434]. The differences between the E2 and EBNA1 structures occur in the loops and connections between the beta strands.


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) · 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 6 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 Viral DNA-binding 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 6 hidden Markov models representing the Viral DNA-binding 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) · UniProtKB KeyWords (KW) · Internal database links ]