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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 (3,139) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 10,440 76,552 4
Proteins 10,351 75,886 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-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) cellular aromatic compound metabolic process 0 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.00000000000001422 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.0000000007122 Least Informative Direct
Biological Process (BP) primary metabolic process 0.000002216 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.000000000002059 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.000000000000003734 Least Informative Direct
Biological Process (BP) biological regulation 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.7167 Least Informative Inherited
Biological Process (BP) response to stimulus 0.7069 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) organelle organization 0.00000001802 Moderately Informative Direct
Biological Process (BP) response to external stimulus 0.09214 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.07642 Moderately Informative Inherited
Biological Process (BP) animal organ development 0.04421 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.2254 Moderately Informative Inherited
Biological Process (BP) cell communication 0.9544 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.001408 Moderately Informative Inherited
Biological Process (BP) DNA metabolic process 0 Informative Direct
Biological Process (BP) response to extracellular stimulus 0.0002408 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0.00008023 Informative Direct
Biological Process (BP) chromosome organization 0 Informative Direct
Biological Process (BP) regulation of organelle organization 0.001571 Informative Inherited
Biological Process (BP) cellular response to DNA damage stimulus 0.002082 Informative Inherited
Biological Process (BP) regeneration 0.0000001425 Highly Informative Direct
Biological Process (BP) cellular response to extracellular stimulus 0.0000149 Highly Informative Direct
Biological Process (BP) regulation of chromosome organization 0.000001444 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0.0000008073 Highly Informative Direct
Molecular Function (MF) hydrolase activity 0 Least Informative Direct
Molecular Function (MF) binding 0.377 Least Informative Inherited
Molecular Function (MF) hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 0 Moderately Informative Direct
Molecular Function (MF) isomerase activity 0 Moderately Informative Direct
Molecular Function (MF) metal ion binding 0.000162 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.000181 Moderately Informative Direct
Molecular Function (MF) anion binding 0.5047 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.001268 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.4787 Moderately Informative Inherited
Molecular Function (MF) magnesium ion binding 0.0000000008189 Informative Direct
Molecular Function (MF) DNA binding 0.000009158 Informative Direct
Molecular Function (MF) ATPase activity 0 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.000008703 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.00001034 Informative Direct
Molecular Function (MF) purine ribonucleoside triphosphate binding 0.000003088 Informative Direct
Molecular Function (MF) ATP binding 0.0000002197 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 0.02584 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 0.00486 Least Informative Inherited
Cellular Component (CC) chromosome 0.000009109 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processAntibiotic resistance0InformativeDirect
Biological processBiological rhythms0.000000771InformativeDirect
Cellular componentCytoplasm0.0000000007068Least InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionNucleotide-binding0Least InformativeDirect
Molecular functionMetal-binding0.0009058Least InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationIsomerase0Moderately InformativeDirect
Post-translational modificationTopoisomerase0Highly InformativeDirect
Post-translational modificationAutocatalytic cleavage0.000578InformativeDirect
Post-translational modificationProtein splicing0.000000000006155Highly 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-coverage) · 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-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]