5CZ1 | pdb_00005cz1

Crystal structure of the catalytic core domain of MMTV integrase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d5cz1d_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Retroviral integrase, catalytic domain	automated matches	MMTV (Mouse mammary tumor virus ) [TaxId: 11757 ],	SCOPe (2.08)
C	d5cz1c1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Retroviral integrase, catalytic domain	automated matches	MMTV (Mouse mammary tumor virus ) [TaxId: 11757 ],	SCOPe (2.08)
C	d5cz1c2	Artifacts	Tags	Tags	Tags	C-terminal Tags	MMTV (Mouse mammary tumor virus ) [TaxId: 11757 ],	SCOPe (2.08)
B	d5cz1b_	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Retroviral integrase, catalytic domain	automated matches	MMTV (Mouse mammary tumor virus ) [TaxId: 11757 ],	SCOPe (2.08)
A	d5cz1a1	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Retroviral integrase, catalytic domain	automated matches	MMTV (Mouse mammary tumor virus ) [TaxId: 11757 ],	SCOPe (2.08)
A	d5cz1a2	Artifacts	Tags	Tags	Tags	C-terminal Tags	MMTV (Mouse mammary tumor virus ) [TaxId: 11757 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Ribonuclease H-like	8068081	3000143	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribonuclease H-like	8068081	3000143	SCOP2B (2022-06-29)
B	SCOP2 Family	Retroviral integrase, catalytic domain	8068080	4000539	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Ribonuclease H-like	8068081	3000143	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8068081	3000143	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	Glyco_hydro_31_2nd	e5cz1D1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (v294.1)
C	Glyco_hydro_31_2nd	e5cz1C1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (v294.1)
B	Glyco_hydro_31_2nd	e5cz1B1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (v294.1)
A	Glyco_hydro_31_2nd	e5cz1A1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Fibronectin type I module-like	T: Fibronectin type I module	F: Glyco_hydro_31_2nd	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
C	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00665	Integrase core domain (rve)	Integrase core domain	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain Pfam:PF02022. This domain is the central catalytic domain. The ca ...	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain Pfam:PF02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain Pfam:PF00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	integrase	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding nucleic acid binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding nucleic acid binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity endopeptidase activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity RNA nuclease activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity RNA-directed DNA polymerase activity RNA binding RNA stem-loop binding pyrophosphatase activity nucleoside triphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides dUTP diphosphatase activity hydrolase activity, acting on acid anhydrides structural constituent of virion structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction establishment of integrated proviral latency viral latency establishment of viral latency viral gene expression viral translational frameshifting viral translation viral genome integration into host DNA biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction establishment of integrated proviral latency viral latency establishment of viral latency viral gene expression viral translational frameshifting viral translation viral genome integration into host DNA nucleobase-containing compound metabolic process DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA integration proteolysis protein metabolic process	viral nucleocapsid viral capsid virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, C, D	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A, B, C, D	IPR036157	dUTPase-like superfamily	Homologous Superfamily
A, B, C, D	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, C, D	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B, C, D	IPR038124	Beta-retroviral matrix superfamily	Homologous Superfamily
A, B, C, D	IPR003322	Beta-retroviral matrix protein	Domain
A, B, C, D	IPR001878	Zinc finger, CCHC-type	Domain
A, B, C, D	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A, B, C, D	IPR010999	Retroviral matrix protein	Homologous Superfamily
A, B, C, D	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B, C, D	IPR001969	Aspartic peptidase, active site	Active Site
A, B, C, D	IPR029054	dUTPase-like	Domain
A, B, C, D	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
A, B, C, D	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B, C, D	IPR018061	Retropepsins	Domain
A, B, C, D	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
A, B, C, D	IPR010661	Reverse transcriptase thumb	Domain
A, B, C, D	IPR002156	Ribonuclease H domain	Domain
A, B, C, D	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B, C, D	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
A, B, C, D	IPR001584	Integrase, catalytic core	Domain
A, B, C, D	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D	IPR033704	dUTPase, trimeric	Domain
A, B, C, D	IPR001037	Integrase, C-terminal, retroviral	Domain
A, B, C, D	IPR034170	Retropepsin-like catalytic domain	Domain
A, B, C, D	IPR000477	Reverse transcriptase domain	Domain
A, B, C, D	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily