SUPERFAMILY 1.75 HMM library and genome assignments server


DNA topoisomerase IV, alpha subunit superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Multi-domain proteins (alpha and beta) [ 56572] (66)
Fold:   DNA topoisomerase IV, alpha subunit [ 56725]
Superfamily:   DNA topoisomerase IV, alpha subunit [ 56726]
Families:   DNA topoisomerase IV, alpha subunit [ 56727]


Superfamily statistics
Genomes (700) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 983 1,101 1
Proteins 972 1,098 1


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)cellular aromatic compound metabolic process1.235e-073.99e-10Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process7.342e-073.176e-09Least InformativeDirect
Biological Process (BP)heterocycle metabolic process1.165e-073.212e-10Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process2.515e-079.704e-10Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.00062390.008418Least InformativeInherited
Biological Process (BP)multicellular organismal process0.013970.01291Least InformativeInherited
Biological Process (BP)single-organism cellular process0.15130.04354Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process3.387e-070.00438Least InformativeInherited
Biological Process (BP)reproduction4.958e-068.28e-09Moderately InformativeDirect
Biological Process (BP)organelle organization0.0042920.02592Moderately InformativeInherited
Biological Process (BP)DNA metabolic process9.994e-131.086e-14InformativeDirect
Biological Process (BP)cell cycle process7.131e-082.544e-10InformativeDirect
Biological Process (BP)cellular process involved in reproduction6.097e-079.271e-11InformativeDirect
Biological Process (BP)chromosome organization5.225e-071.165e-06InformativeDirect
Biological Process (BP)DNA recombination01.538e-06Highly InformativeDirect
Biological Process (BP)meiosis9.969e-120Highly InformativeDirect

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) cellular aromatic compound metabolic process 3.99e-10 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 3.176e-09 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 3.212e-10 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 9.704e-10 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.008418 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.01291 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.04354 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.00438 Least Informative Inherited
Biological Process (BP) reproduction 8.28e-09 Moderately Informative Direct
Biological Process (BP) organelle organization 0.02592 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 1.086e-14 Informative Direct
Biological Process (BP) cell cycle process 2.544e-10 Informative Direct
Biological Process (BP) cellular process involved in reproduction 9.271e-11 Informative Direct
Biological Process (BP) chromosome organization 1.165e-06 Informative Direct
Biological Process (BP) DNA recombination 1.538e-06 Highly Informative Direct
Biological Process (BP) meiosis 0 Highly 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

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 topoisomerase (ATP-hydrolyzing)0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processMeiosis0InformativeDirect
Cellular componentNucleus5.501e-07Least InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionNucleotide-binding9.869e-05Least InformativeDirect
Molecular functionMetal-binding0.0001279Least InformativeDirect
Molecular functionMagnesium4.501e-13Moderately InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationTopoisomerase0Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR002815 SSF56726 Protein matches
Abstract

This entry represents Spo11, a meiotic recombination protein found in eukaryotes, and subunit A of topoisomerase VI, a type IIB topoisomerase found predominantly in archaea [PubMed10545127, PubMed12618182]. These two types of proteins share structural homology.

DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. They can be divided into two classes: type I enzymes (, topoisomerases I, III and V) break single-strand DNA, and type II enzymes (, topoisomerases II, IV and VI) break double-strand DNA [PubMed12596227]. Topoisomerase VI is a type IIB enzymes that assembles as a heterotetramer, consisting of two A subunits required for DNA cleavage and two B subunits required for ATP hydrolysis. The B subunit is structurally similar to the ATPase domain of type IIA topoisomerases, but the A subunit is distinct, and instead shares homology with the Spo11 protein.

Spo11 is a meiosis-specific protein that is responsible for the initiation of recombination through the formation of DNA double-strand breaks by a type II DNA topoisomerase-like activity. Spo11 acts in conjunction with several other proteins, including Rec102 in yeast, to bring about meiotic recombination [PubMed11805049].

More information about this protein can be found at Protein of the Month: DNA Topoisomerase.


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 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 DNA topoisomerase IV, alpha subunit 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 DNA topoisomerase IV, alpha subunit 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 ]