5ZEN

Crystal structure of human topoisomerase II beta in complex with DNA: a new quaternary conformation showing opening of the protein-linked DNA-gate

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DNA_topoisoIV_1st	e5zenA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DNA_topoisoIV_1st	ECOD (1.6)
A	DNA_topoisoIV_3rd	e5zenA3	A: alpha bundles	X: alpha-helical domain in type II DNA topoisomerase (From Topology)	H: alpha-helical domain in type II DNA topoisomerase (From Topology)	T: alpha-helical domain in type II DNA topoisomerase	F: DNA_topoisoIV_3rd	ECOD (1.6)
A	TOPRIM_C	e5zenA5	A: a+b two layers	X: SSHS domain	H: SSHS domain in type II DNA topoisomerase (From Topology)	T: SSHS domain in type II DNA topoisomerase	F: TOPRIM_C	ECOD (1.6)
A	DNA_topoisoIV_2nd_1	e5zenA2	A: a+b two layers	X: a+b domain in type II DNA topoisomerase (From Topology)	H: a+b domain in type II DNA topoisomerase (From Topology)	T: a+b domain in type II DNA topoisomerase	F: DNA_topoisoIV_2nd_1	ECOD (1.6)
A	DNA_gyraseB_C	e5zenA4	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: Toprim domain	F: DNA_gyraseB_C	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01751	Toprim domain (Toprim)	Toprim domain	-	Family
A	PF16898	C-terminal associated domain of TOPRIM (TOPRIM_C)	C-terminal associated domain of TOPRIM	-	Family
A	PF00521	DNA gyrase/topoisomerase IV, subunit A (DNA_topoisoIV)	DNA gyrase/topoisomerase IV, subunit A	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	DNA (5'-D(PAPGPCPCPGPAPGPC)-3')	-	-	-
A	DNA topoisomerase 2-beta	protein-containing complex binding chromatin binding binding ribonucleoprotein complex binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding protein-containing complex binding chromatin binding binding ribonucleoprotein complex binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding ATP-dependent activity, acting on DNA isomerase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA topoisomerase activity DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity catalytic activity ATP-dependent activity cation binding metal ion binding	regulation of cellular process viral life cycle positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process positive regulation of nucleobase-containing compound metabolic process positive regulation of viral genome replication cellular metabolic process primary metabolic process regulation of cellular process viral life cycle positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process positive regulation of nucleobase-containing compound metabolic process positive regulation of viral genome replication cellular metabolic process primary metabolic process regulation of cellular metabolic process single stranded viral RNA replication via double stranded DNA intermediate positive regulation of RNA metabolic process biosynthetic process viral genome replication metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process regulation of single stranded viral RNA replication via double stranded DNA intermediate cellular biosynthetic process positive regulation of biological process RNA metabolic process positive regulation of cellular metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of single stranded viral RNA replication via double stranded DNA intermediate positive regulation of biosynthetic process viral RNA genome replication viral process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of viral process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process regulation of viral process regulation of viral life cycle positive regulation of RNA biosynthetic process regulation of viral genome replication cellular process positive regulation of cellular biosynthetic process developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development leukocyte differentiation cellular response to stimulus regulation of double-strand break repair response to stimulus regulation of cellular response to stress positive regulation of response to stimulus positive regulation of DNA repair cellular response to stress response to stress regulation of response to stress regulation of double-strand break repair via nonhomologous end joining DNA repair double-strand break repair positive regulation of double-strand break repair via nonhomologous end joining double-strand break repair via nonhomologous end joining DNA metabolic process positive regulation of double-strand break repair regulation of DNA repair positive regulation of DNA metabolic process DNA damage response regulation of response to stimulus regulation of DNA metabolic process sexual reproduction homologous recombination reproductive process resolution of meiotic recombination intermediates meiotic cell cycle process cellular component organization meiosis I meiotic nuclear division cell cycle cellular component organization or biogenesis reciprocal homologous recombination cell cycle process meiotic cell cycle DNA recombination organelle fission reciprocal meiotic recombination nuclear division organelle organization meiosis I cell cycle process chromosome organization DNA conformation change DNA topological change cellular senescence axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis system development plasma membrane bounded cell projection organization nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron development cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to chemical stimulus response to chemical head development forebrain development animal organ development brain development central nervous system development cellular response to nitrogen compound cellular response to ATP response to organonitrogen compound response to endogenous stimulus response to organophosphorus cellular response to organic cyclic compound response to nitrogen compound response to ATP response to purine-containing compound cellular response to endogenous stimulus cellular response to organonitrogen compound response to organic cyclic compound neuron migration cell migration cell motility nuclear chromosome segregation sister chromatid segregation chromosome segregation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle cytoplasm cytosol nucleoplasm protein-containing complex ribonucleoprotein complex
C	DNA (5'-D(PAPGPCPTPCPGPGPCP*T)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001154	DNA topoisomerase II, eukaryotic-type	Family
A	IPR018522	DNA topoisomerase, type IIA, conserved site	Conserved Site
A	IPR013506	DNA topoisomerase, type IIA, subunit B, domain 2	Domain
A	IPR013760	DNA topoisomerase, type IIA-like domain superfamily	Homologous Superfamily
A	IPR013758	DNA topoisomerase, type IIA, domain A, alpha-beta	Homologous Superfamily
A	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A	IPR006171	TOPRIM domain	Domain
A	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
A	IPR034157	DNA topoisomerase 2, TOPRIM domain	Domain
A	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A	IPR001241	DNA topoisomerase, type IIA	Family
A	IPR050634	DNA Topoisomerase II Enzyme	Family
A	IPR012542	DTHCT	Domain
A	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily
A	IPR013757	DNA topoisomerase, type IIA, alpha-helical domain superfamily	Homologous Superfamily
A	IPR013759	DNA topoisomerase, type IIA, subunit B, C-terminal	Homologous Superfamily
A	IPR031660	C-terminal associated domain of TOPRIM	Domain
A	IPR002205	DNA topoisomerase, type IIA, domain A	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q02880	myeloid leukemia prostate intraepithelial neoplasia chronic monocytic leukemia acute myeloid leukemia dermatomyositis medulloblastoma lung cancer chronic obstructive pulmonary disease lymphoplasmacytic lymphoma open-angle glaucoma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.