4GA5 | pdb_00004ga5

Crystal structure of AMP phosphorylase C-terminal deletion mutant in the apo-form

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	CDC48_N	e4ga5H4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
H	Glycos_trans_3N	e4ga5H2	A: alpha arrays	X: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase-N	F: Glycos_trans_3N	ECOD (1.6)
H	PYNP_C	e4ga5H3	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Pyrimidine nucleoside phosphorylase C-terminal domain	F: PYNP_C	ECOD (1.6)
H	Glycos_transf_3	e4ga5H1	A: a/b three-layered sandwiches	X: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	F: Glycos_transf_3	ECOD (1.6)
G	CDC48_N	e4ga5G4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
G	Glycos_trans_3N	e4ga5G2	A: alpha arrays	X: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase-N	F: Glycos_trans_3N	ECOD (1.6)
G	PYNP_C	e4ga5G3	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Pyrimidine nucleoside phosphorylase C-terminal domain	F: PYNP_C	ECOD (1.6)
G	Glycos_transf_3	e4ga5G1	A: a/b three-layered sandwiches	X: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	F: Glycos_transf_3	ECOD (1.6)
F	CDC48_N	e4ga5F4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
F	Glycos_trans_3N	e4ga5F2	A: alpha arrays	X: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase-N	F: Glycos_trans_3N	ECOD (1.6)
F	PYNP_C	e4ga5F3	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Pyrimidine nucleoside phosphorylase C-terminal domain	F: PYNP_C	ECOD (1.6)
F	Glycos_transf_3	e4ga5F1	A: a/b three-layered sandwiches	X: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	F: Glycos_transf_3	ECOD (1.6)
E	CDC48_N	e4ga5E4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
E	Glycos_trans_3N	e4ga5E2	A: alpha arrays	X: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase-N	F: Glycos_trans_3N	ECOD (1.6)
E	PYNP_C	e4ga5E3	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Pyrimidine nucleoside phosphorylase C-terminal domain	F: PYNP_C	ECOD (1.6)
E	Glycos_transf_3	e4ga5E1	A: a/b three-layered sandwiches	X: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	F: Glycos_transf_3	ECOD (1.6)
D	CDC48_N	e4ga5D4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
D	Glycos_trans_3N	e4ga5D2	A: alpha arrays	X: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase-N	F: Glycos_trans_3N	ECOD (1.6)
D	PYNP_C	e4ga5D3	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Pyrimidine nucleoside phosphorylase C-terminal domain	F: PYNP_C	ECOD (1.6)
D	Glycos_transf_3	e4ga5D1	A: a/b three-layered sandwiches	X: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	F: Glycos_transf_3	ECOD (1.6)
C	CDC48_N	e4ga5C4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
C	Glycos_trans_3N	e4ga5C2	A: alpha arrays	X: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase-N	F: Glycos_trans_3N	ECOD (1.6)
C	PYNP_C	e4ga5C3	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Pyrimidine nucleoside phosphorylase C-terminal domain	F: PYNP_C	ECOD (1.6)
C	Glycos_transf_3	e4ga5C1	A: a/b three-layered sandwiches	X: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	F: Glycos_transf_3	ECOD (1.6)
B [auth A]	CDC48_N	e4ga5A4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
B [auth A]	Glycos_trans_3N	e4ga5A2	A: alpha arrays	X: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase-N	F: Glycos_trans_3N	ECOD (1.6)
B [auth A]	PYNP_C	e4ga5A3	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Pyrimidine nucleoside phosphorylase C-terminal domain	F: PYNP_C	ECOD (1.6)
B [auth A]	Glycos_transf_3	e4ga5A1	A: a/b three-layered sandwiches	X: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	F: Glycos_transf_3	ECOD (1.6)
A [auth B]	CDC48_N	e4ga5B4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: CDC48_N	ECOD (1.6)
A [auth B]	Glycos_trans_3N	e4ga5B2	A: alpha arrays	X: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase-N	F: Glycos_trans_3N	ECOD (1.6)
A [auth B]	PYNP_C	e4ga5B3	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Pyrimidine nucleoside phosphorylase C-terminal domain	F: PYNP_C	ECOD (1.6)
A [auth B]	Glycos_transf_3	e4ga5B1	A: a/b three-layered sandwiches	X: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	F: Glycos_transf_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
H	1.20.970.50	Mainly Alpha	Up-down Bundle	Transferase, Pyrimidine Nucleoside Phosphorylase	Chain A, domain 3	CATH (4.3.0)
H	3.40.1030.10	Alpha Beta	3-Layer(aba) Sandwich	Pyrimidine Nucleoside Phosphorylase	Chain A, domain 2	CATH (4.3.0)
H	3.90.1170.30	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	CATH (4.3.0)
G	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
G	1.20.970.50	Mainly Alpha	Up-down Bundle	Transferase, Pyrimidine Nucleoside Phosphorylase	Chain A, domain 3	CATH (4.3.0)
G	3.40.1030.10	Alpha Beta	3-Layer(aba) Sandwich	Pyrimidine Nucleoside Phosphorylase	Chain A, domain 2	CATH (4.3.0)
G	3.90.1170.30	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	CATH (4.3.0)
F	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
F	1.20.970.50	Mainly Alpha	Up-down Bundle	Transferase, Pyrimidine Nucleoside Phosphorylase	Chain A, domain 3	CATH (4.3.0)
F	3.40.1030.10	Alpha Beta	3-Layer(aba) Sandwich	Pyrimidine Nucleoside Phosphorylase	Chain A, domain 2	CATH (4.3.0)
F	3.90.1170.30	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	CATH (4.3.0)
E	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
E	1.20.970.50	Mainly Alpha	Up-down Bundle	Transferase, Pyrimidine Nucleoside Phosphorylase	Chain A, domain 3	CATH (4.3.0)
E	3.40.1030.10	Alpha Beta	3-Layer(aba) Sandwich	Pyrimidine Nucleoside Phosphorylase	Chain A, domain 2	CATH (4.3.0)
E	3.90.1170.30	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	CATH (4.3.0)
D	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
D	1.20.970.50	Mainly Alpha	Up-down Bundle	Transferase, Pyrimidine Nucleoside Phosphorylase	Chain A, domain 3	CATH (4.3.0)
D	3.40.1030.10	Alpha Beta	3-Layer(aba) Sandwich	Pyrimidine Nucleoside Phosphorylase	Chain A, domain 2	CATH (4.3.0)
D	3.90.1170.30	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	CATH (4.3.0)
C	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
C	1.20.970.50	Mainly Alpha	Up-down Bundle	Transferase, Pyrimidine Nucleoside Phosphorylase	Chain A, domain 3	CATH (4.3.0)
C	3.40.1030.10	Alpha Beta	3-Layer(aba) Sandwich	Pyrimidine Nucleoside Phosphorylase	Chain A, domain 2	CATH (4.3.0)
C	3.90.1170.30	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	CATH (4.3.0)
B [auth A]	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
B [auth A]	1.20.970.50	Mainly Alpha	Up-down Bundle	Transferase, Pyrimidine Nucleoside Phosphorylase	Chain A, domain 3	CATH (4.3.0)
B [auth A]	3.40.1030.10	Alpha Beta	3-Layer(aba) Sandwich	Pyrimidine Nucleoside Phosphorylase	Chain A, domain 2	CATH (4.3.0)
B [auth A]	3.90.1170.30	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	CATH (4.3.0)
A [auth B]	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.3.0)
A [auth B]	1.20.970.50	Mainly Alpha	Up-down Bundle	Transferase, Pyrimidine Nucleoside Phosphorylase	Chain A, domain 3	CATH (4.3.0)
A [auth B]	3.40.1030.10	Alpha Beta	3-Layer(aba) Sandwich	Pyrimidine Nucleoside Phosphorylase	Chain A, domain 2	CATH (4.3.0)
A [auth B]	3.90.1170.30	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth A], C, D, E, A [auth B], B [auth A], C, D, E, F, G, H	PF00591	Glycosyl transferase family, a/b domain (Glycos_transf_3)	Glycosyl transferase family, a/b domain	This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate.	Domain
A [auth B], B [auth A], C, D, E, A [auth B], B [auth A], C, D, E, F, G, H	PF02885	Glycosyl transferase family, helical bundle domain (Glycos_trans_3N)	Glycosyl transferase family, helical bundle domain	This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate.	Domain
A [auth B], B [auth A], C, D, E, A [auth B], B [auth A], C, D, E, F, G, H	PF07831	Pyrimidine nucleoside phosphorylase C-terminal domain (PYNP_C)	Pyrimidine nucleoside phosphorylase C-terminal domain	This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases [1,2]. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside ...	This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases [1,2]. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP, Swiss:P77826) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as E. coli thymidine phosphorylase (TP, Swiss:P07650) [1]. The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], B [auth A], C, D, E, A [auth B], B [auth A], C, D, E, F, G, H	Putative thymidine phosphorylase	1,4-alpha-oligoglucan phosphorylase activity glycosyltransferase activity transferase activity hexosyltransferase activity catalytic activity ion binding binding anion binding phosphate ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding cation binding 1,4-alpha-oligoglucan phosphorylase activity glycosyltransferase activity transferase activity hexosyltransferase activity catalytic activity ion binding binding anion binding phosphate ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding cation binding AMP binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding pentosyltransferase activity	glycosyl compound metabolic process pyrimidine-containing compound metabolic process deoxyribonucleoside metabolic process carbohydrate derivative metabolic process primary metabolic process pyrimidine nucleoside metabolic process nucleoside metabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process metabolic process cellular process pyrimidine deoxyribonucleoside metabolic process pyrimidine nucleobase metabolic process glycosyl compound metabolic process pyrimidine-containing compound metabolic process deoxyribonucleoside metabolic process carbohydrate derivative metabolic process primary metabolic process pyrimidine nucleoside metabolic process nucleoside metabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process metabolic process cellular process pyrimidine deoxyribonucleoside metabolic process pyrimidine nucleobase metabolic process nucleobase metabolic process ribose phosphate metabolic process ribonucleotide catabolic process catabolic process organophosphate catabolic process nucleoside phosphate catabolic process AMP metabolic process purine ribonucleoside monophosphate catabolic process purine nucleoside monophosphate catabolic process purine ribonucleoside monophosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process purine nucleoside monophosphate metabolic process phosphate-containing compound metabolic process ribonucleoside monophosphate catabolic process purine ribonucleotide catabolic process phosphorus metabolic process nucleoside monophosphate metabolic process nucleotide catabolic process nucleoside phosphate metabolic process purine nucleotide catabolic process carbohydrate derivative catabolic process nucleoside monophosphate catabolic process purine-containing compound catabolic process nucleotide metabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process organophosphate metabolic process AMP catabolic process purine ribonucleotide metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], B [auth A], C, D, E, A [auth B], B [auth A], C, D, E, F, G, H	IPR000053	Thymidine/pyrimidine-nucleoside phosphorylase	Family
A [auth B], B [auth A], C, D, E, A [auth B], B [auth A], C, D, E, F, G, H	IPR017713	AMP phosphorylase	Family
A [auth B], B [auth A], C, D, E, A [auth B], B [auth A], C, D, E, F, G, H	IPR035902	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily	Homologous Superfamily
A [auth B], B [auth A], C, D, E, A [auth B], B [auth A], C, D, E, F, G, H	IPR036320	Glycosyl transferase family 3, N-terminal domain superfamily	Homologous Superfamily
A [auth B], B [auth A], C, D, E, A [auth B], B [auth A], C, D, E, F, G, H	IPR036566	Pyrimidine nucleoside phosphorylase-like, C-terminal domain superfamily	Homologous Superfamily
A [auth B], B [auth A], C, D, E, A [auth B], B [auth A], C, D, E, F, G, H	IPR000312	Glycosyl transferase, family 3	Domain
A [auth B], B [auth A], C, D, E, A [auth B], B [auth A], C, D, E, F, G, H	IPR017872	Pyrimidine-nucleoside phosphorylase, conserved site	Conserved Site
A [auth B], B [auth A], C, D, E, A [auth B], B [auth A], C, D, E, F, G, H	IPR017459	Glycosyl transferase family 3, N-terminal domain	Domain
A [auth B], B [auth A], C, D, E, A [auth B], B [auth A], C, D, E, F, G, H	IPR013466	Thymidine phosphorylase/AMP phosphorylase	Family
A [auth B], B [auth A], C, D, E, A [auth B], B [auth A], C, D, E, F, G, H	IPR013102	Pyrimidine nucleoside phosphorylase, C-terminal	Domain