Prokaryotic type I DNA topoisomerase superfamily

SCOP classification

• Root: SCOP hierarchy in SUPERFAMILY [ 0] (11)
• Class: Multi-domain proteins (alpha and beta) [ 56572] (66)
• Fold: Prokaryotic type I DNA topoisomerase [ 56711]
• Superfamily: Prokaryotic type I DNA topoisomerase [ 56712]
• Families: Prokaryotic type I DNA topoisomerase [ 56713] (3)

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Superfamily statistics

	Genomes (3,201)	Uniprot 2018_03 genome	PDB chains (SCOP 1.75)
Domains	5,686	45,154	8
Proteins	5,633	44,971	8

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Functional annotation

• General category: Information
• Detailed category: DNA replication/repair

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Enzyme Commission (EC)

Highlighted in gray are those with FDR_all>0.001

	EC term	FDR (all)	IC level	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	DNA helicase	0	1.162	--	DIRECT
Enzyme Commission (EC)	Other isomerases	0	1.446	--	DIRECT
Enzyme Commission (EC)	Hydrolases	0.91	0.04271	--	INHERITED FROM: Acting on acid anhydrides; involved in cellular an || DNA helicase || Acting on acid anhydrides
Enzyme Commission (EC)	Isomerases	0	0.5914	Least Informative	DIRECT
Enzyme Commission (EC)	Acting on acid anhydrides	0.000005958	0.6408	Least Informative	DIRECT
Enzyme Commission (EC)	Acting on acid anhydrides; involved in cellular an	0.0000000000002586	0.8971	Moderately Informative	DIRECT
Enzyme Commission (EC)	Sole sub-subclass for isomerases that do not belon	1	1.481	Informative	INHERITED FROM: DNA topoisomerase
Enzyme Commission (EC)	DNA topoisomerase	0	1.861	Highly Informative	DIRECT

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Arabidopsis Plant Ontology (AP)

Highlighted in gray are those with FDR_all>0.001

	AP term	FDR (all)	IC level	SDAP level	Annotation (direct or inherited)
Plant ANatomical entity (PAN)	petiole	0	0.7287	--	DIRECT
Plant ANatomical entity (PAN)	stalk	0	0.7019	--	DIRECT
Plant ANatomical entity (PAN)	plant embryo	0	0.5969	--	DIRECT
Plant ANatomical entity (PAN)	leaf lamina	0	0.7057	--	DIRECT
Plant ANatomical entity (PAN)	epidermal cell	0	0.2569	--	DIRECT
Plant ANatomical entity (PAN)	inflorescence branch	0	0.6366	--	DIRECT
Plant ANatomical entity (PAN)	stem internode	0	0.6495	--	DIRECT
Plant ANatomical entity (PAN)	phyllome apex	0	0.7019	--	DIRECT
Plant ANatomical entity (PAN)	shoot internode	0	0.6463	--	DIRECT
Plant ANatomical entity (PAN)	phyllome	0	0.3809	--	DIRECT
Plant ANatomical entity (PAN)	corolla	0	0.594	--	DIRECT
Plant ANatomical entity (PAN)	shoot epidermis	0	0.2691	--	DIRECT
Plant ANatomical entity (PAN)	stem	0	0.577	--	DIRECT
Plant ANatomical entity (PAN)	perianth	0	0.5448	--	DIRECT
Plant ANatomical entity (PAN)	cardinal organ part	0	0.51	--	DIRECT
Plant ANatomical entity (PAN)	shoot system	0	0.05747	--	DIRECT
Plant ANatomical entity (PAN)	shoot epidermal cell	0	0.276	--	DIRECT
Plant ANatomical entity (PAN)	cauline leaf	0	0.7019	--	DIRECT
Plant ANatomical entity (PAN)	lamina	0	0.7057	--	DIRECT
Plant ANatomical entity (PAN)	plant cell	0	0.1489	--	DIRECT
Plant ANatomical entity (PAN)	epidermis	0	0.2464	--	DIRECT
Plant ANatomical entity (PAN)	reproductive shoot system	0	0.4141	--	DIRECT
Plant ANatomical entity (PAN)	leaf lamina base	0	0.7094	--	DIRECT
Plant ANatomical entity (PAN)	petal	0	0.594	--	DIRECT
Plant ANatomical entity (PAN)	calyx	0	0.5715	--	DIRECT
Plant ANatomical entity (PAN)	pedicel	0	0.6366	--	DIRECT
Plant ANatomical entity (PAN)	inflorescence axis	0	0.6366	--	DIRECT
Plant ANatomical entity (PAN)	collective plant structure	0	0.01577	--	DIRECT
Plant ANatomical entity (PAN)	portion of plant tissue	0	0.1892	--	DIRECT
Plant ANatomical entity (PAN)	leaf apex	0	0.7094	--	DIRECT
Plant ANatomical entity (PAN)	plant axis	0	0.3881	--	DIRECT
Plant ANatomical entity (PAN)	multi-tissue plant structure	0	0.2691	--	DIRECT
Plant ANatomical entity (PAN)	root	0	0.5579	--	DIRECT
Plant ANatomical entity (PAN)	plant organ	0	0.2816	--	DIRECT
Plant ANatomical entity (PAN)	vascular leaf	0	0.5246	--	DIRECT
Plant ANatomical entity (PAN)	branch	0	0.6366	--	DIRECT
Plant ANatomical entity (PAN)	sepal	0	0.5715	--	DIRECT
Plant ANatomical entity (PAN)	stomatal complex	0	0.2774	--	DIRECT
Plant ANatomical entity (PAN)	collective leaf structure	0	0.55	--	DIRECT
Plant ANatomical entity (PAN)	shoot apex	0	0.5633	--	DIRECT
Plant ANatomical entity (PAN)	organ lamina	1	0.7057	--	INHERITED FROM: leaf lamina base || leaf lamina
Plant ANatomical entity (PAN)	collective plant organ structure	1	0.04502	--	INHERITED FROM: inflorescence axis || calyx || flower || root system || inflorescence || root || perianth || stem || leaf || phyllome || shoot internode || sepal || vascular leaf || petiole || petal || reproductive shoot system || shoot apex || leaf apex || collective phyllome structure || guard cell || cauline leaf || leaf lamina || shoot epidermal cell || corolla || pedicel || stomatal complex || phyllome apex || stem internode || inflorescence branch || shoot axis || shoot system || leaf lamina base || collective leaf structure || branch || shoot epidermis
Plant ANatomical entity (PAN)	plant structure	1	0	--	INHERITED FROM: perianth || root || calyx || inflorescence axis || flower || lamina || collective plant structure || plant embryo || leaf || shoot internode || phyllome || cardinal organ part || multi-tissue plant structure || guard cell || cauline leaf || reproductive shoot system || shoot apex || leaf apex || leaf lamina base || branch || collective leaf structure || stem internode || inflorescence branch || shoot system || portion of plant tissue || stomatal complex || plant organ || stem || whole plant || epidermis || root system || inflorescence || cardinal part of multi-tissue plant structure || petiole || stalk || vascular leaf || sepal || epidermal cell || leaf lamina || shoot epidermal cell || corolla || plant axis || collective phyllome structure || petal || plant cell || seed || shoot epidermis || phyllome apex || shoot axis || pedicel
Plant ANatomical entity (PAN)	phyllome lamina	1	0.7057	--	INHERITED FROM: leaf lamina base || leaf lamina
Plant ANatomical entity (PAN)	leaf	0	0.5053	Least Informative	DIRECT
Plant ANatomical entity (PAN)	seed	0	0.6087	Least Informative	DIRECT
Plant ANatomical entity (PAN)	guard cell	0	0.2774	Least Informative	DIRECT
Plant ANatomical entity (PAN)	collective phyllome structure	0	0.4648	Least Informative	DIRECT
Plant ANatomical entity (PAN)	whole plant	0	0.4218	Least Informative	DIRECT
Plant ANatomical entity (PAN)	shoot axis	0	0.4735	Least Informative	DIRECT
Plant ANatomical entity (PAN)	root system	0	0.5346	Least Informative	DIRECT
Plant ANatomical entity (PAN)	cardinal part of multi-tissue plant structure	0	0.5029	Least Informative	DIRECT
Plant ANatomical entity (PAN)	flower	0	0.4337	Least Informative	DIRECT
Plant ANatomical entity (PAN)	inflorescence	0	0.5969	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	1 main shoot growth stage	0	0.3937	--	DIRECT
Plant structure DEvelopment stage (PDE)	leaf production stage	0	0.3937	--	DIRECT
Plant structure DEvelopment stage (PDE)	whole plant development stage	0	0.1968	--	DIRECT
Plant structure DEvelopment stage (PDE)	plant organ development stage	0	0.08108	--	DIRECT
Plant structure DEvelopment stage (PDE)	plant embryo stage	0	0.2833	--	DIRECT
Plant structure DEvelopment stage (PDE)	collective plant organ structure development stage	0	0.03771	--	DIRECT
Plant structure DEvelopment stage (PDE)	floral organ formation stage	0	0.0937	--	DIRECT
Plant structure DEvelopment stage (PDE)	floral organ differentiation stage	0	0.0937	--	DIRECT
Plant structure DEvelopment stage (PDE)	corolla development stage	0	0.1981	--	DIRECT
Plant structure DEvelopment stage (PDE)	flowering stage	0	0.2162	--	DIRECT
Plant structure DEvelopment stage (PDE)	collective phyllome structure development stage	0	0.0937	--	DIRECT
Plant structure DEvelopment stage (PDE)	phyllome development stage	0	0.4754	--	DIRECT
Plant structure DEvelopment stage (PDE)	sporophyte vegetative stage	0	0.2036	--	DIRECT
Plant structure DEvelopment stage (PDE)	reproductive shoot system development stage	0	0.05008	--	DIRECT
Plant structure DEvelopment stage (PDE)	life of whole plant stage	1	0.2022	--	INHERITED FROM: sporophyte vegetative stage || C globular stage || LP.10 ten leaves visible stage || E expanded cotyledon stage || LP.12 twelve leaves visible stage || F mature embryo stage || LP.04 four leaves visible stage || D bilateral stage || LP.06 six leaves visible stage || LP.08 eight leaves visible stage || LP.02 two leaves visible stage || plant embryo stage || leaf production stage || 1 main shoot growth stage
Plant structure DEvelopment stage (PDE)	flower development stage	1	0.07083	--	INHERITED FROM: corolla development stage || flowering stage || floral organ differentiation stage || floral organ formation stage
Plant structure DEvelopment stage (PDE)	shoot system development stage	1	0.04053	--	INHERITED FROM: phyllome development stage || reproductive shoot system development stage || floral organ formation stage || floral organ differentiation stage || flowering stage || corolla development stage || plant organ development stage || 4 leaf senescence stage
Plant structure DEvelopment stage (PDE)	leaf development stage	1	0.4754	--	INHERITED FROM: 4 leaf senescence stage
Plant structure DEvelopment stage (PDE)	sporophyte development stage	1	0.2022	--	INHERITED FROM: LP.08 eight leaves visible stage || LP.12 twelve leaves visible stage || E expanded cotyledon stage || LP.10 ten leaves visible stage || LP.06 six leaves visible stage || sporophyte vegetative stage || C globular stage || leaf production stage || 1 main shoot growth stage || D bilateral stage || F mature embryo stage || LP.04 four leaves visible stage || plant embryo stage || LP.02 two leaves visible stage
Plant structure DEvelopment stage (PDE)	4 leaf senescence stage	0	0.478	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	D bilateral stage	0	0.3729	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.02 two leaves visible stage	0	0.5603	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.04 four leaves visible stage	0	0.4338	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	F mature embryo stage	0	0.4088	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	E expanded cotyledon stage	0	0.353	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.10 ten leaves visible stage	0	0.513	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.08 eight leaves visible stage	0	0.586	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.12 twelve leaves visible stage	0	0.5666	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	C globular stage	0	0.3937	Least Informative	DIRECT
Plant structure DEvelopment stage (PDE)	LP.06 six leaves visible stage	0	0.5243	Least Informative	DIRECT

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Enzyme Commission (EC)

Highlighted in gray are those with FDR_all>0.001

	EC term	FDR (all)	IC level	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Enzymes altering nucleic acid conformation	0	1.806	--	DIRECT
Enzyme Commission (EC)	Acting on ATP; involved in cellular and subcellular movement	0.0000000000004327	1.196	--	DIRECT
Enzyme Commission (EC)	Hydrolases	0.8162	0.3541	Least Informative	INHERITED FROM: DNA helicase || Acting on ATP; involved in cellular and subcellular movement || Acting on acid anhydrides
Enzyme Commission (EC)	Isomerases	0	0.8446	Moderately Informative	DIRECT
Enzyme Commission (EC)	Acting on acid anhydrides	0.00000002077	0.9562	Moderately Informative	DIRECT
Enzyme Commission (EC)	DNA helicase	0	1.475	Informative	DIRECT
Enzyme Commission (EC)	Isomerases altering macromolecular conformation	0	1.651	Informative	DIRECT
Enzyme Commission (EC)	DNA topoisomerase	0	2.174	Highly Informative	DIRECT

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InterPro annotation

• Cross references: IPR000380 SSF56712 Protein matches
• Abstract:

  This entry describes the core region of type IA topoisomerases, which are highly conserved enzymes that are structurally distinct from type IB enzymes. The structures of both topoisomerases I and III have been elucidated, and consist of four domains that together form a toroidal molecule with a central hole that is large enough to accommodate single- and double-stranded DNA [11239459]. It is believed that the domains transiently separate from one another to allow the entrance and exit of DNA strands.

  More information about this protein can be found at Protein of the Month: DNA Topoisomerase.

InterPro database

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