SUPERFAMILY 1.75 HMM library and genome assignments server

Please note: Superfamily is currently under maintenance and some functionality may be limited. Please bear with us as we fix these problems.


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 (3,132) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 10,412 74,059 4
Proteins 10,322 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)cellular component organization or biogenesis00.00006964Least InformativeDirect
Biological Process (BP)developmental process00.08515Least InformativeInherited
Biological Process (BP)multicellular organismal process00.1682Least InformativeInherited
Biological Process (BP)single-organism cellular process00.9972Least InformativeInherited
Biological Process (BP)organ development00.00008689Moderately InformativeDirect
Biological Process (BP)cell differentiation00.0003487Moderately InformativeDirect
Cellular Component (CC)intracellular non-membrane-bounded organelle00.000003165Least InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle00.00008452Least InformativeDirect
Cellular Component (CC)chromosome00.00000001029InformativeDirect

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 component organization or biogenesis 0.00006964 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0 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) single-organism metabolic process 0.00000000002017 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0000002313 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.1682 Least Informative Inherited
Biological Process (BP) developmental process 0.08515 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.9972 Least Informative Inherited
Biological Process (BP) localization 0.1655 Least Informative Inherited
Biological Process (BP) organ development 0.00008689 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0003487 Moderately Informative Direct
Biological Process (BP) organic cyclic compound catabolic process 0 Moderately Informative Direct
Biological Process (BP) organophosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) organonitrogen compound catabolic process 0 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound 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) cellular catabolic process 0 Moderately Informative Direct
Biological Process (BP) organelle organization 0.004904 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.1411 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.1489 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.1217 Moderately Informative Inherited
Biological Process (BP) purine ribonucleoside metabolic process 0 Informative Direct
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) nucleobase-containing compound catabolic process 0 Informative Direct
Biological Process (BP) organophosphate catabolic process 0 Informative Direct
Biological Process (BP) glycosyl compound catabolic process 0 Informative Direct
Biological Process (BP) carbohydrate derivative catabolic process 0 Informative Direct
Biological Process (BP) nucleoside monophosphate metabolic process 0.000000000001688 Informative Direct
Biological Process (BP) chromosome organization 0.000000001544 Informative Direct
Biological Process (BP) nucleoside triphosphate metabolic process 0.000000009752 Informative Direct
Biological Process (BP) generation of neurons 0.000128 Informative Direct
Biological Process (BP) localization of cell 0.0002082 Informative Direct
Biological Process (BP) locomotion 0.0006853 Informative Direct
Biological Process (BP) cell projection organization 0.001307 Informative Inherited
Biological Process (BP) cellular component morphogenesis 0.01605 Informative Inherited
Biological Process (BP) central nervous system development 0.001033 Informative Inherited
Biological Process (BP) purine ribonucleotide metabolic process 0.05543 Informative Inherited
Biological Process (BP) cellular component movement 0.00503 Informative Inherited
Biological Process (BP) chromosome segregation 0 Highly Informative Direct
Biological Process (BP) purine ribonucleoside triphosphate catabolic process 0 Highly Informative Direct
Biological Process (BP) ATP metabolic 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) purine ribonucleoside catabolic process 0 Highly Informative Direct
Biological Process (BP) neuron projection development 0.000009009 Highly Informative Direct
Biological Process (BP) cell part morphogenesis 0.00001226 Highly Informative Direct
Biological Process (BP) cell morphogenesis involved in differentiation 0.00001666 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0.000000000004847 Least Informative Direct
Molecular Function (MF) binding 0.04502 Least Informative Inherited
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0 Moderately Informative Direct
Molecular Function (MF) cation binding 0.0652 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.648 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.3099 Moderately Informative Inherited
Molecular Function (MF) nucleoside-triphosphatase activity 0 Informative Direct
Molecular Function (MF) magnesium ion binding 0.000000000003686 Informative Direct
Molecular Function (MF) DNA binding 0.00000002672 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.000001544 Informative Direct
Molecular Function (MF) purine ribonucleoside binding 0.000002193 Informative Direct
Molecular Function (MF) nucleotide binding 0.00002157 Informative Direct
Molecular Function (MF) ATP binding 0.0000001214 Highly Informative Direct
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.000003165 Least Informative Direct
Cellular Component (CC) intracellular membrane-bounded organelle 0.00008452 Least Informative Direct
Cellular Component (CC) protein complex 0.0001288 Least Informative Direct
Cellular Component (CC) intracellular organelle part 0.5784 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.00007438 Moderately Informative Direct
Cellular Component (CC) chromosome 0.00000001029 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAntibiotic resistance0InformativeDirect
Cellular componentCytoplasm0.00000003876Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMetal-binding0.00008072Least InformativeDirect
Molecular functionATP-binding0Moderately InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionMagnesium0Moderately InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationTopoisomerase0Highly InformativeDirect
Post-translational modificationAutocatalytic cleavage0.0003466InformativeDirect
Post-translational modificationProtein splicing0.000000000004929Highly 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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]