4M1E | pdb_00004m1e

Crystal structure of purine nucleoside phosphorylase I from Planctomyces limnophilus DSM 3776, NYSGRC Target 029364.

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)
F	d4m1ef_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Planctopirus limnophila DSM 3776 ) [TaxId: 521674 ],	SCOPe (2.08)
E [auth D]	d4m1ed_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Planctopirus limnophila DSM 3776 ) [TaxId: 521674 ],	SCOPe (2.08)
D [auth E]	d4m1ee_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Planctopirus limnophila DSM 3776 ) [TaxId: 521674 ],	SCOPe (2.08)
C	d4m1ec_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Planctopirus limnophila DSM 3776 ) [TaxId: 521674 ],	SCOPe (2.08)
B	d4m1eb_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Planctopirus limnophila DSM 3776 ) [TaxId: 521674 ],	SCOPe (2.08)
A	d4m1ea_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	automated matches	automated matches	(Planctopirus limnophila DSM 3776 ) [TaxId: 521674 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Purine and uridine phosphorylases	8061240	3000626	SCOP2B (2022-06-29)
E [auth D]	SCOP2B Superfamily	Purine and uridine phosphorylases	8061240	3000626	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Purine and uridine phosphorylases	8061240	3000626	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Purine and uridine phosphorylases	8061240	3000626	SCOP2B (2022-06-29)
B	SCOP2 Family	Purine and uridine phosphorylases	8061239	4000573	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Purine and uridine phosphorylases	8061240	3000626	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Purine and uridine phosphorylases	8061240	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)
F		e4m1eF1	A: L-aspartase middle domain-like	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like	T: Cu_amine_oxidN2	F:	ECOD (20:10:01)
E [auth D]		e4m1eD1	A: L-aspartase middle domain-like	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like	T: Cu_amine_oxidN2	F:	ECOD (20:10:01)
D [auth E]		e4m1eE1	A: L-aspartase middle domain-like	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like	T: Cu_amine_oxidN2	F:	ECOD (20:10:01)
C		e4m1eC1	A: L-aspartase middle domain-like	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like	T: Cu_amine_oxidN2	F:	ECOD (20:10:01)
B		e4m1eB1	A: beta-propeller-like	X: beta-propeller	H: 6-bladed	T:	F:	ECOD (20:10:01)
A		e4m1eA1	A: L-aspartase middle domain-like	X: L-aspartase middle domain-like	H: L-aspartase middle domain-like	T: Cu_amine_oxidN2	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
E [auth D]	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
D [auth E]	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)
B	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
A	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 [auth E], E [auth D], A, B, C, D [auth E], E [auth D], F	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 [auth E], E [auth D], A, B, C, D [auth E], E [auth D], F	Purine nucleoside phosphorylase	pentosyltransferase activity glycosyltransferase activity purine-nucleoside phosphorylase activity transferase activity catalytic activity	nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process carbohydrate derivative metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process nucleoside metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D [auth E], E [auth D], A, B, C, D [auth E], E [auth D], F	IPR035994	Nucleoside phosphorylase superfamily	Homologous Superfamily
A, B, C, D [auth E], E [auth D], A, B, C, D [auth E], E [auth D], F	IPR011268	Purine nucleoside phosphorylase	Family
A, B, C, D [auth E], E [auth D], A, B, C, D [auth E], E [auth D], F	IPR018099	Purine phosphorylase, family 2, conserved site	Conserved Site
A, B, C, D [auth E], E [auth D], A, B, C, D [auth E], E [auth D], F	IPR011270	Purine nucleoside phosphorylase I, inosine/guanosine-specific	Family
A, B, C, D [auth E], E [auth D], A, B, C, D [auth E], E [auth D], F	IPR000845	Nucleoside phosphorylase domain	Domain

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.