4TS9

Crystal structure of wild type E. Coli purine nucleoside phosphorylase with 6 FMC molecules

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4ts9a_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Purine nucleoside phosphorylase, PNP	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d4ts9b_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Purine nucleoside phosphorylase, PNP	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d4ts9c_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Purine nucleoside phosphorylase, PNP	(Escherichia coli ) [TaxId: 562 ],	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	8037965	3000626	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Purine and uridine phosphorylases	8037965	3000626	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Purine and uridine phosphorylases	8037965	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	e4ts9A1	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	e4ts9B1	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	e4ts9C1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	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	Purine nucleoside phosphorylase DeoD-type	guanosine phosphorylase activity pentosyltransferase activity glycosyltransferase activity transferase activity catalytic activity purine-nucleoside phosphorylase activity identical protein binding protein binding binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process carbohydrate derivative catabolic process glycosyl compound metabolic process catabolic process purine nucleoside catabolic process carbohydrate derivative metabolic process primary metabolic process glycosyl compound catabolic process purine-containing compound catabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process carbohydrate derivative catabolic process glycosyl compound metabolic process catabolic process purine nucleoside catabolic process carbohydrate derivative metabolic process primary metabolic process glycosyl compound catabolic process purine-containing compound catabolic process nucleoside metabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule catabolic process nucleobase-containing small molecule metabolic process nucleoside catabolic process small molecule metabolic process metabolic process small molecule catabolic process purine nucleoside metabolic process nucleobase-containing small molecule interconversion purine nucleoside interconversion	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR018016	Nucleoside phosphorylase, conserved site	Conserved Site
A, B, C	IPR004402	Purine nucleoside phosphorylase DeoD-type	Family
A, B, C	IPR035994	Nucleoside phosphorylase superfamily	Homologous Superfamily
A, B, C	IPR000845	Nucleoside phosphorylase domain	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A, C	Purine nucleoside phosphorylase DeoD-type M-CSA #375	Purine nucleoside phosphorylase is involved in purine metabolism, metabolising adenosine into adenine and guanosine into guanine, for example. Also works on inosine. These pathways allow the cell to produce nucleotide monophosphates when they cannot synthesise them de novo. The enzyme catalyses the reversible phosphorolytic cleavage of the glycosidic bond of purine nucleosides with the overall reaction: beta-purine nucleoside + orthophosphate <-> purine base + alpha-D-pentose-1-phosphate	Defined by 7 residues: GLY:A-20ARG:A-24ARG:A-87SER:A-90ASP:A-204ARG:A-217ARG:C-43 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.4.2.1 (PDB Primary Data) Search M-CSA Motif + EC 2.4.2.1

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.