SUPERFAMILY 1.75 HMM library and genome assignments server


DNA breaking-rejoining enzymes superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   DNA breaking-rejoining enzymes [ 56348]
Superfamily:   DNA breaking-rejoining enzymes [ 56349] (2)
Families:   Lambda integrase-like, catalytic core [ 56350] (5)
  Eukaryotic DNA topoisomerase I, catalytic core [ 56361]


Superfamily statistics
Genomes (3,089) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 26,020 184,312 34
Proteins 25,954 184,077 34


Functional annotation
General category Information
Detailed category DNA replication/repair

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)heterocycle metabolic process0.0044230.000000000003137Least InformativeInherited
Biological Process (BP)cellular aromatic compound metabolic process0.0045440.000000000004953Least InformativeInherited
Biological Process (BP)organic cyclic compound metabolic process0.0065560.00000000003284Least InformativeInherited
Biological Process (BP)nitrogen compound metabolic process0.01130.0000000003974Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.007850.0000000221Least InformativeInherited
Biological Process (BP)DNA metabolic process0.0000081540InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) heterocycle metabolic process 0.000000000003137 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.000000000004953 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00000000003284 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0000000221 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.0000000003974 Least Informative Direct
Biological Process (BP) multi-organism process 0.0009302 Moderately Informative Direct
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) multi-organism cellular process 0.00000168 Highly Informative Direct
Biological Process (BP) symbiosis, encompassing mutualism through parasitism 0.000002859 Highly Informative Direct
Molecular Function (MF) binding 1 Least Informative Inherited
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.004826 Moderately Informative Inherited
Molecular Function (MF) chromatin binding 0.0001112 Informative Direct
Molecular Function (MF) DNA binding 0.0002679 Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.001398 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 0.06987 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) chromosome 0.0000005673 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Least InformativeDirect
Enzyme Commission (EC)Sole sub-subclass for isomerases that do not belon1InformativeInherited
Enzyme Commission (EC)DNA topoisomerase0Highly InformativeDirect

Document: EC 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

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Isomerases0Moderately InformativeDirect
Enzyme Commission (EC)DNA topoisomerase0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processCell cycle0Moderately InformativeDirect
Biological processVirus entry into host cell0InformativeDirect
Biological processDNA recombination0InformativeDirect
Biological processChromosome partition0Highly InformativeDirect
Biological processDNA integration0Highly InformativeDirect
Biological processViral genome integration0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Post-translational modificationIsomerase0.00264Moderately InformativeInherited
Post-translational modificationTopoisomerase0Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011010 SSF56349 Protein matches
Abstract

Phage integrases are enzymes that mediate unidirectional site-specific recombination between two DNA recognition sequences, the phage attachment site, attP, and the bacterial attachment site, attB [PubMed14687564]. Integrases may be grouped into two major families, the tyrosine recombinases and the serine recombinases, based on their mode of catalysis. Tyrosine family integrases, such as lambda integrase, utilise a catalytic tyrosine to mediate strand cleavage, tend to recognize longer attP sequences, and require other proteins encoded by the phage or the host bacteria.

The 356 amino acid lambda integrase consists of two domains: an N-terminal domain that includes residues 1-64 and is responsible for binding the arm-type sites of attP, and a C-terminal domain (CTD) that binds the lower affinity core-type sites and contains the catalytic site. The CTD can be further divided into the core-type binding domain (residues 65-169) and the catalytic core domain (170-356), the later representing this entry. The catalytic core adopts an alpha3-beta3-alpha4 fold, where one side of the beta sheet is exposed.

The recombinases Cre from phage P1, XerD from Escherichia coli and Flp from yeast are members of the tyrosine recombinase family, and have a two-domain motif resembling that of lambda integrase, as well as sharing a conserved binding mechanism [PubMed12560475]. The structural fold of their catalytic core domains resemble that of Lambda integrase

The catalytic core of the eukaryotic DNA topoisomerase I shares significant structural similarity with the bacteriophage family of DNA integrases [PubMed9488644]. Topoisomerases I promote the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination.


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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · 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 9 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 DNA breaking-rejoining enzymes 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 9 hidden Markov models representing the DNA breaking-rejoining enzymes 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-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]