1BRW
THE CRYSTAL STRUCTURE OF PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE IN A CLOSED CONFORMATION
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2 Family | Pyrimidine nucleoside phosphorylase C-terminal domain | 8022641 | 4001133 | SCOP2 (2022-06-29) |
A | SCOP2 Family | Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | 8025194 | 4000984 | SCOP2 (2022-06-29) |
A | SCOP2 Family | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | 8031834 | 4003843 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Pyrimidine nucleoside phosphorylase C-terminal domain | 8035021 | 3000876 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | 8037573 | 3000348 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | 8044212 | 3001630 | SCOP2 (2022-06-29) |
B | SCOP2B Superfamily | Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | 8037573 | 3000348 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Pyrimidine nucleoside phosphorylase C-terminal domain | 8035021 | 3000876 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | 8044212 | 3001630 | 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 | Glycos_trans_3N | e1brwA1 | 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 | PYNP_C | e1brwA2 | 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 | Glycos_transf_3 | e1brwA3 | 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 | Glycos_trans_3N | e1brwB1 | 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 | PYNP_C | e1brwB2 | 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 | Glycos_transf_3 | e1brwB3 | 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) |
---|---|---|---|---|---|---|
A | 3.90.1170.30 | Alpha Beta | Alpha-Beta Complex | Aldehyde Oxidoreductase | domain 3 | CATH (4.3.0) |
A | 3.40.1030.10 | Alpha Beta | 3-Layer(aba) Sandwich | Pyrimidine Nucleoside Phosphorylase | Chain A, domain 2 | CATH (4.3.0) |
A | 1.20.970.10 | Mainly Alpha | Up-down Bundle | Transferase, Pyrimidine Nucleoside Phosphorylase | Chain A, domain 3 | CATH (4.3.0) |
B | 3.90.1170.30 | Alpha Beta | Alpha-Beta Complex | Aldehyde Oxidoreductase | domain 3 | CATH (4.3.0) |
B | 3.40.1030.10 | Alpha Beta | 3-Layer(aba) Sandwich | Pyrimidine Nucleoside Phosphorylase | Chain A, domain 2 | CATH (4.3.0) |
B | 1.20.970.10 | Mainly Alpha | Up-down Bundle | Transferase, Pyrimidine Nucleoside Phosphorylase | Chain A, domain 3 | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF00591 | Glycosyl transferase family, a/b domain (Glycos_transf_3) | Glycosyl transferase family, a/b domain | - | Family | |
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 | |
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 ... | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
pyrimidine-nucleoside phosphorylase M-CSA #91 | Pyrimidine-nucleoside phosphorylase (Py-NP) catalyses the reversible phosphorylation of both uridine and thymidine in the nucleotide synthesis salvage pathway. It is found in all lower organisms whilst in higher organisms such phosphorylases are specific to those individual nucleosides. Nevertheless, Py-NPs share 40% sequence similarity with thymidine specific phosphorylase seen in higher organisms, a prominent drug target in treating breast cancer. | Defined by 5 residues: HIS:A-82ASP:A-161ARG:A-168SER:A-183LYS:A-187 | EC: 2.4.2.2 (PDB Primary Data) |