2D4L | pdb_00002d4l

Crystal structure of truncated in C-terminal M-PMV dUTPase

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2d4la_	All beta proteins	beta-clip	dUTPase-like	automated matches	automated matches	(Mason-Pfizer monkey virus ) [TaxId: 11855 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	dUTPase-like	8073094	3001957	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)
A	dUTPase	e2d4lA1	A: beta barrels	X: beta-clip	H: dUTPase-like (From Topology)	T: dUTPase-like	F: dUTPase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.70.40.10	Mainly Beta	Distorted Sandwich	Deoxyuridine 5'-Triphosphate Nucleotidohydrolase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00692	dUTPase (dUTPase)	dUTPase	dUTPase hydrolyses dUTP to dUMP and pyrophosphate.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DU	DNA binding binding nucleic acid binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity catalytic activity endopeptidase activity pyrophosphatase activity nucleoside triphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides dUTP diphosphatase activity DNA binding binding nucleic acid binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity catalytic activity endopeptidase activity 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	viral gene expression viral process viral translational frameshifting viral translation nucleoside phosphate metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process viral gene expression viral process viral translational frameshifting viral translation nucleoside phosphate metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process proteolysis protein metabolic process macromolecule metabolic process	viral nucleocapsid viral capsid virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A	IPR036157	dUTPase-like superfamily	Homologous Superfamily
A	IPR050195	Primate lentivirus group Gag polyprotein-like	Domain
A	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A	IPR038124	Beta-retroviral matrix superfamily	Homologous Superfamily
A	IPR003322	Beta-retroviral matrix protein	Domain
A	IPR001878	Zinc finger, CCHC-type	Domain
A	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A	IPR010999	Retroviral matrix protein	Homologous Superfamily
A	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A	IPR001969	Aspartic peptidase, active site	Active Site
A	IPR029054	dUTPase-like	Domain
A	IPR000467	G-patch domain	Domain
A	IPR018061	Retropepsins	Domain
A	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A	IPR033704	dUTPase, trimeric	Domain
A	IPR034170	Retropepsin-like catalytic domain	Domain
A	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210

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 R01GM157729.