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 (742) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 1,087 1,550 1
Proteins 1,075 1,545 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 process0.00000014510.000000000006504Least InformativeDirect
Biological Process (BP)nitrogen compound metabolic process0.00000084860.00000000007694Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.00000013940.000000000005075Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis0.000710.000002605Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.00000029560.00000000001843Least InformativeDirect
Biological Process (BP)multicellular organismal process0.012990.02774Least InformativeInherited
Biological Process (BP)single-organism metabolic process0.074220.0002173Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process0.00000033520.01176Least InformativeInherited
Biological Process (BP)single-organism cellular process0.43040.07535Least InformativeInherited
Biological Process (BP)single-organism organelle organization0.0000013240.00000004374Moderately InformativeDirect
Biological Process (BP)cell cycle process0.000000070870.00000000006166InformativeDirect
Biological Process (BP)organelle fission0.00000000045050InformativeDirect
Biological Process (BP)cell division0.0000000056960.000000000000003707InformativeDirect
Biological Process (BP)chromosome organization0.002360.1518InformativeInherited
Biological Process (BP)nuclear division0.00000000024360Highly InformativeDirect
Biological Process (BP)DNA recombination00Highly InformativeDirect
Biological Process (BP)meiotic cell cycle0.000000000048120Highly 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 0.000000000006504 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0.00000000007694 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0002173 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.000000000005075 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.000002605 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.00000000001843 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.02774 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.01176 Least Informative Inherited
Biological Process (BP) response to stimulus 0.3347 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.07535 Least Informative Inherited
Biological Process (BP) reproductive process 0.0005432 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.00009808 Moderately Informative Direct
Biological Process (BP) single-organism organelle organization 0.00000004374 Moderately Informative Direct
Biological Process (BP) DNA repair 0.00001082 Informative Direct
Biological Process (BP) cell cycle process 0.00000000006166 Informative Direct
Biological Process (BP) organelle fission 0 Informative Direct
Biological Process (BP) cell division 0.000000000000003707 Informative Direct
Biological Process (BP) chromosome organization 0.1518 Informative Inherited
Biological Process (BP) nuclear division 0 Highly Informative Direct
Biological Process (BP) double-strand break repair 0.0000000004375 Highly Informative Direct
Biological Process (BP) DNA recombination 0 Highly Informative Direct
Biological Process (BP) meiotic cell cycle 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 componentNucleus0.0000000004043Least InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionMetal-binding0.000009622Least InformativeDirect
Molecular functionMagnesium9.203e-16Moderately 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 ]