3QPB

Crystal Structure of Streptococcus Pyogenes Uridine Phosphorylase Reveals a Subclass of the NP-I Superfamily

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)
A	d3qpba_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)
B	d3qpbb_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)
C	d3qpbc_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)
D	d3qpbd_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)
E	d3qpbe_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)
F	d3qpbf_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)
G	d3qpbg_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)
H	d3qpbh_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)
I	d3qpbi_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)
J	d3qpbj_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)
K	d3qpbk_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)
L	d3qpbl_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)
M	d3qpbm_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)
N	d3qpbn_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)
O	d3qpbo_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)
P	d3qpbp_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)
Q	d3qpbq_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)
R	d3qpbr_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Streptococcus pyogenes serotype M6 ) [TaxId: 301450 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Purine and uridine phosphorylases	8074245	3000626	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Purine and uridine phosphorylases	8074245	3000626	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Purine and uridine phosphorylases	8074245	3000626	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Purine and uridine phosphorylases	8074245	3000626	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Purine and uridine phosphorylases	8074245	3000626	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Purine and uridine phosphorylases	8074245	3000626	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Purine and uridine phosphorylases	8074245	3000626	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Purine and uridine phosphorylases	8074245	3000626	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Purine and uridine phosphorylases	8074245	3000626	SCOP2B (2022-06-29)
J	SCOP2 Family	Purine and uridine phosphorylases	8074244	4000573	SCOP2 (2022-06-29)
J	SCOP2 Superfamily	Purine and uridine phosphorylases	8074245	3000626	SCOP2 (2022-06-29)
K	SCOP2B Superfamily	Purine and uridine phosphorylases	8074245	3000626	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Purine and uridine phosphorylases	8074245	3000626	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Purine and uridine phosphorylases	8074245	3000626	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Purine and uridine phosphorylases	8074245	3000626	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Purine and uridine phosphorylases	8074245	3000626	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Purine and uridine phosphorylases	8074245	3000626	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Purine and uridine phosphorylases	8074245	3000626	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	Purine and uridine phosphorylases	8074245	3000626	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	PNP_UDP_1	e3qpbA1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
B	PNP_UDP_1	e3qpbB1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
C	PNP_UDP_1	e3qpbC1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
D	PNP_UDP_1	e3qpbD1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
E	PNP_UDP_1	e3qpbE1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
F	PNP_UDP_1	e3qpbF1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
G	PNP_UDP_1	e3qpbG1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
H	PNP_UDP_1	e3qpbH1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
I	PNP_UDP_1	e3qpbI1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
J	PNP_UDP_1	e3qpbJ1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
K	PNP_UDP_1	e3qpbK1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
L	PNP_UDP_1	e3qpbL1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
M	PNP_UDP_1	e3qpbM1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
N	PNP_UDP_1	e3qpbN1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
O	PNP_UDP_1	e3qpbO1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
P	PNP_UDP_1	e3qpbP1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
Q	PNP_UDP_1	e3qpbQ1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
R	PNP_UDP_1	e3qpbR1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
B	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
C	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
D	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
E	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
F	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
G	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
H	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
I	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
J	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
K	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
L	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
M	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
N	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
O	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
P	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
Q	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
R	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	PF01048	Phosphorylase superfamily (PNP_UDP_1)	Phosphorylase superfamily	Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase)	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	Uridine phosphorylase	pentosyltransferase activity glycosyltransferase activity uridine phosphorylase activity transferase activity catalytic activity pyrimidine-nucleoside phosphorylase activity	nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process pyrimidine-containing compound salvage nucleobase-containing compound metabolic process ribonucleotide biosynthetic process organic substance biosynthetic process phosphate-containing compound metabolic process UMP metabolic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process cellular metabolic compound salvage nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process pyrimidine-containing compound salvage nucleobase-containing compound metabolic process ribonucleotide biosynthetic process organic substance biosynthetic process phosphate-containing compound metabolic process UMP metabolic process small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process cellular metabolic compound salvage nucleoside phosphate metabolic process pyrimidine-containing compound metabolic process pyrimidine ribonucleoside monophosphate metabolic process cellular metabolic process primary metabolic process nucleotide metabolic process organic cyclic compound metabolic process biosynthetic process pyrimidine ribonucleoside monophosphate biosynthetic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process metabolic process pyrimidine nucleoside monophosphate biosynthetic process ribose phosphate metabolic process pyrimidine ribonucleotide salvage pyrimidine nucleotide salvage nucleotide salvage UMP salvage organic substance metabolic process UMP biosynthetic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process nucleobase-containing small molecule metabolic process pyrimidine-containing compound biosynthetic process nucleoside monophosphate metabolic process pyrimidine ribonucleotide metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process organonitrogen compound metabolic process nucleobase-containing compound biosynthetic process nucleoside monophosphate biosynthetic process organophosphate metabolic process cellular process ribonucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process organonitrogen compound catabolic process carbohydrate derivative catabolic process glycosyl compound metabolic process catabolic process glycosyl compound catabolic process nucleoside metabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process nucleobase-containing small molecule catabolic process nucleoside catabolic process small molecule catabolic process organic substance catabolic process organophosphate catabolic process nucleoside phosphate catabolic process nucleotide catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR018016	Nucleoside phosphorylase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR035994	Nucleoside phosphorylase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR010058	Uridine phosphorylase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR000845	Nucleoside phosphorylase domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.