SUPERFAMILY 1.75 HMM library and genome assignments server

Type II DNA topoisomerase superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Multi-domain proteins (alpha and beta) [ 56572] (66)
Fold:   Type II DNA topoisomerase [ 56718]
Superfamily:   Type II DNA topoisomerase [ 56719]
Families:   Type II DNA topoisomerase [ 56720] (2)


Superfamily statistics
Genomes (3,133) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 10,430 74,059 4
Proteins 10,340 73,909 4


Functional annotation
General category coiled coil
Detailed category This is a complex coiled arrangement. The details of which will appear on this page shortly (some coiled coil details are being checked before they are included on the site). If you want to see examples of the states please click here here. If you require further details urgently please contact Owen Rackham

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)single-organism cellular process00.0000006053Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis00.0001011Least InformativeDirect
Biological Process (BP)multicellular organismal process00.132Least InformativeInherited
Biological Process (BP)developmental process00.08509Least InformativeInherited
Biological Process (BP)organ development00.00007994Moderately InformativeDirect
Biological Process (BP)cell differentiation00.0003894Moderately InformativeDirect
Cellular Component (CC)non-membrane-bounded organelle00.000003406Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle00.00005327Least InformativeDirect
Cellular Component (CC)chromosome00.000000006032InformativeDirect

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) single-organism cellular process 0.0000006053 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0001011 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism metabolic process 0.0000000005138 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0000001579 Least Informative Direct
Biological Process (BP) localization 0.1863 Least Informative Inherited
Biological Process (BP) developmental process 0.08509 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.132 Least Informative Inherited
Biological Process (BP) organ development 0.00007994 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0003894 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) nucleobase-containing small molecule metabolic process 0 Moderately Informative Direct
Biological Process (BP) carbohydrate derivative metabolic process 0 Moderately Informative Direct
Biological Process (BP) nervous system development 0.1515 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.1496 Moderately Informative Inherited
Biological Process (BP) single-organism organelle organization 0.02994 Moderately Informative Inherited
Biological Process (BP) nucleobase-containing compound catabolic process 0 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0 Informative Direct
Biological Process (BP) organophosphate catabolic process 0 Informative Direct
Biological Process (BP) purine ribonucleoside metabolic process 0 Informative Direct
Biological Process (BP) organonitrogen compound catabolic process 0 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0.0000000000107 Informative Direct
Biological Process (BP) chromosome organization 0.000000001575 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 0.00000003619 Informative Direct
Biological Process (BP) generation of neurons 0.0001333 Informative Direct
Biological Process (BP) localization of cell 0.0001817 Informative Direct
Biological Process (BP) locomotion 0.0006788 Informative Direct
Biological Process (BP) cell projection organization 0.025 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.0227 Informative Inherited
Biological Process (BP) central nervous system development 0.001164 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.07048 Informative Inherited
Biological Process (BP) cellular component movement 0.07761 Informative Inherited
Biological Process (BP) purine ribonucleoside catabolic process 0 Highly Informative Direct
Biological Process (BP) purine nucleoside triphosphate catabolic process 0 Highly Informative Direct
Biological Process (BP) purine ribonucleotide catabolic process 0 Highly Informative Direct
Biological Process (BP) nucleoside monophosphate catabolic process 0 Highly Informative Direct
Biological Process (BP) ribonucleoside triphosphate catabolic process 0 Highly Informative Direct
Biological Process (BP) chromosome segregation 0.000000000001269 Highly Informative Direct
Biological Process (BP) neuron projection development 0.00000916 Highly Informative Direct
Biological Process (BP) cell projection morphogenesis 0.00001106 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 0.00001693 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.00000000000461 Least Informative Direct
Molecular Function (MF) binding 0.04939 Least Informative Inherited
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.0004271 Moderately Informative Direct
Molecular Function (MF) small molecule binding 0.0009144 Moderately Informative Direct
Molecular Function (MF) anion binding 0.651 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.3271 Moderately Informative Inherited
Molecular Function (MF) cation binding 0.06511 Moderately Informative Inherited
Molecular Function (MF) nucleoside-triphosphatase activity 0 Informative Direct
Molecular Function (MF) magnesium ion binding 0.000000000003889 Informative Direct
Molecular Function (MF) DNA binding 0.00000002956 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.000001555 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 0.000002194 Informative Direct
Molecular Function (MF) nucleotide binding 0.00002213 Informative Direct
Molecular Function (MF) ATP binding 0.0000001223 Highly Informative Direct
Cellular Component (CC) non-membrane-bounded organelle 0.000003406 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00005327 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.5502 Least Informative Inherited
Cellular Component (CC) protein complex 0.1034 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.00002747 Moderately Informative Direct
Cellular Component (CC) chromosome 0.000000006032 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

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)cell physiology variant0Least InformativeDirect

Document: WP 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

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)antiinfectives for systemic use0.00000001595Least InformativeDirect
Drugbank ATC_code (DB)sensory organs0.0001045Least InformativeDirect
Drugbank ATC_code (DB)antibacterials for systemic use0.00000000009253Moderately InformativeDirect
Drugbank ATC_code (DB)antiinfectives0.000000007782Moderately InformativeDirect
Drugbank ATC_code (DB)fluoroquinolones0InformativeDirect
Drugbank ATC_code (DB)quinolone antibacterials0InformativeDirect
Drugbank ATC_code (DB)antiinfectives1InformativeInherited
Drugbank ATC_code (DB)ciprofloxacin0.00000002908Highly InformativeDirect
Drugbank ATC_code (DB)ofloxacin0.00000002908Highly InformativeDirect
Drugbank ATC_code (DB)ciprofloxacin0.00000002908Highly InformativeDirect

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAntibiotic resistance0InformativeDirect
Cellular componentCytoplasm0.00000003797Least InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMetal-binding0.0001204Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationTopoisomerase0Highly InformativeDirect
Post-translational modificationAutocatalytic cleavage0.0003461InformativeDirect
Post-translational modificationProtein splicing0.000000000004914Highly InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR013760 SSF56719 Protein matches
Abstract

Type IIA topoisomerases together manage chromosome integrity and topology in cells. Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively; this topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions (differs between eukaryotic and bacterial enzymes), domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA [PubMed8982450].

Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication [PubMed16023670]. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB.

This entry represents the C-terminal of subunit B (gyrB and parE) and the N-terminal of subunit A (gyrA and parC) of bacterial gyrase and topoisomerase IV, and the equivalent central region in eukaryotic topoisomerase II composed of a single polypeptide.

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) · Worm Phenotype (WP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · 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 2 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 Type II DNA topoisomerase 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 2 hidden Markov models representing the Type II DNA topoisomerase 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) · Worm Phenotype (WP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · Internal database links ]