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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 (748) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 1,094 3,608 1
Proteins 1,082 3,586 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 process0.000008620.00000000006482Least InformativeDirect
Biological Process (BP)cellular nitrogen compound metabolic process0.000016410.0000000002522Least InformativeDirect
Biological Process (BP)macromolecule metabolic process0.000029750.00000002531Least InformativeDirect
Biological Process (BP)primary metabolic process0.00044390.000001062Least InformativeDirect
Biological Process (BP)heterocycle metabolic process0.0000087620.00000000005606Least InformativeDirect
Biological Process (BP)organic cyclic compound metabolic process0.000014890.0000000001655Least InformativeDirect
Biological Process (BP)single-organism cellular process0.12560.002401Least InformativeInherited
Biological Process (BP)cellular component organization or biogenesis0.0013940.00004547Least InformativeInherited
Biological Process (BP)reproduction0.000024660.0000000001239Moderately InformativeDirect
Biological Process (BP)organelle organization0.000032920.000000009321Moderately InformativeDirect
Biological Process (BP)DNA metabolic process0.0000000007050.0000000129InformativeDirect
Biological Process (BP)cell cycle process0.0000052950.000000000001811InformativeDirect
Biological Process (BP)single organism reproductive process0.000001950.000000000101InformativeDirect
Biological Process (BP)nuclear division0.0000000017190Highly InformativeDirect
Biological Process (BP)DNA recombination0.0000000000003920.000004132Highly InformativeDirect
Biological Process (BP)meiotic cell cycle0.0000000016110Highly 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 0.00000000006482 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.0000000002522 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000002531 Least Informative Direct
Biological Process (BP) primary metabolic process 0.000001062 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.00000000005606 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.00004547 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0000000001655 Least Informative Direct
Biological Process (BP) response to stimulus 0.2449 Least Informative Inherited
Biological Process (BP) single-organism cellular process 0.002401 Least Informative Inherited
Biological Process (BP) reproduction 0.0000000001239 Moderately Informative Direct
Biological Process (BP) organelle organization 0.000000009321 Moderately Informative Direct
Biological Process (BP) cellular response to stress 0.0000429 Moderately Informative Direct
Biological Process (BP) DNA metabolic process 0.0000000129 Informative Direct
Biological Process (BP) cellular response to DNA damage stimulus 0.0000005672 Informative Direct
Biological Process (BP) cell cycle process 0.000000000001811 Informative Direct
Biological Process (BP) single organism reproductive process 0.000000000101 Informative Direct
Biological Process (BP) nuclear division 0 Highly Informative Direct
Biological Process (BP) double-strand break repair 0.0000000001892 Highly Informative Direct
Biological Process (BP) DNA recombination 0.000004132 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processMeiosis0InformativeDirect
Cellular componentNucleus0.0000000001215Least InformativeDirect
Molecular functionMagnesium0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Post-translational modificationHydrolase0.0009152Least InformativeDirect
Post-translational modificationDNA-binding0Moderately 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) · 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) · UniProtKB KeyWords (KW) · Internal database links ]