3DMP | pdb_00003dmp

2.6 A crystal structure of uracil phosphoribosyltransferase from Burkholderia pseudomallei

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	d3dmpd1	Alpha and beta proteins (a/b)	PRTase-like	PRTase-like	Phosphoribosyltransferases (PRTases)	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
D	d3dmpd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
C	d3dmpc1	Alpha and beta proteins (a/b)	PRTase-like	PRTase-like	Phosphoribosyltransferases (PRTases)	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
C	d3dmpc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
B	d3dmpb1	Alpha and beta proteins (a/b)	PRTase-like	PRTase-like	Phosphoribosyltransferases (PRTases)	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
B	d3dmpb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
A	d3dmpa1	Alpha and beta proteins (a/b)	PRTase-like	PRTase-like	Phosphoribosyltransferases (PRTases)	automated matches	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)
A	d3dmpa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Pseudomonas pseudomallei (Burkholderia pseudomallei ) [TaxId: 28450 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	PRTase-like	8083047	3000060	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PRTase-like	8083047	3000060	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PRTase-like	8083047	3000060	SCOP2B (2022-06-29)
A	SCOP2 Family	Phosphoribosyltransferases (PRTases)	8083046	4000253	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PRTase-like	8083047	3000060	SCOP2 (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		e3dmpD1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: RasGEF	F:	ECOD (20:10:01)
C		e3dmpC1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: RasGEF	F:	ECOD (20:10:01)
B		e3dmpB1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: RasGEF	F:	ECOD (20:10:01)
A		e3dmpA1	A: Profilin-like	X: sensor domains	H: sensor domains	T: PIN	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.2020	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	3.40.50.2020	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.40.50.2020	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.40.50.2020	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF14681	Uracil phosphoribosyltransferase (UPRTase)	Uracil phosphoribosyltransferase	This family includes the enzyme uracil phosphoribosyltransferase (EC:2.4.2.9). This enzyme catalyzes the first step of UMP biosynthesis.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Uracil phosphoribosyltransferase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding pentosyltransferase activity glycosyltransferase activity transferase activity catalytic activity uracil phosphoribosyltransferase activity guanyl nucleotide binding GTP binding nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding pentosyltransferase activity glycosyltransferase activity transferase activity catalytic activity uracil phosphoribosyltransferase activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding	pyrimidine-containing compound metabolic process pyrimidine nucleobase salvage nucleobase biosynthetic process uracil metabolic process pyrimidine nucleobase biosynthetic process primary metabolic process pyrimidine-containing compound salvage uracil biosynthetic process nucleobase-containing compound metabolic process metabolic compound salvage pyrimidine nucleobase metabolic process biosynthetic process uracil salvage nucleobase-containing small molecule metabolic process nucleobase metabolic process pyrimidine-containing compound metabolic process pyrimidine nucleobase salvage nucleobase biosynthetic process uracil metabolic process pyrimidine nucleobase biosynthetic process primary metabolic process pyrimidine-containing compound salvage uracil biosynthetic process nucleobase-containing compound metabolic process metabolic compound salvage pyrimidine nucleobase metabolic process biosynthetic process uracil salvage nucleobase-containing small molecule metabolic process nucleobase metabolic process small molecule metabolic process metabolic process cellular process pyrimidine-containing compound biosynthetic process ribose phosphate metabolic process nucleotide biosynthetic process pyrimidine ribonucleotide salvage carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process pyrimidine nucleotide salvage nucleotide salvage ribonucleotide biosynthetic process UMP salvage UMP biosynthetic process ribonucleotide metabolic process phosphate-containing compound metabolic process UMP metabolic process phosphorus metabolic process nucleoside monophosphate metabolic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process pyrimidine ribonucleoside monophosphate metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process nucleoside monophosphate biosynthetic process pyrimidine ribonucleoside monophosphate biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process pyrimidine nucleoside monophosphate biosynthetic process ribonucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR050054	Uracil phosphoribosyltransferase/Adenine phosphoribosyltransferase	Family
A, B, C, D	IPR005765	Uracil phosphoribosyl transferase	Family
A, B, C, D	IPR000836	Phosphoribosyltransferase domain	Domain
A, B, C, D	IPR029057	Phosphoribosyltransferase-like	Homologous Superfamily
A, B, C, D	IPR034332	Uracil phosphoribosyltransferase, bacterial-type	Family

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.