DB code: S00375

RLCP classification 2.40.18500.20 : Phosphorolysis
CATH domain 3.40.50.1580 : Rossmann fold Catalytic domain
E.C. 2.4.2.1
CSA 1ula
M-CSA 1ula
MACiE M0017

CATH domain Related DB codes (homologues)
3.40.50.1580 : Rossmann fold S00510 S00376

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam RefSeq
P55859 Purine nucleoside phosphorylase
PNP
EC 2.4.2.1
Inosine phosphorylase
PF01048 (PNP_UDP_1)
[Graphical View]
P00491 Purine nucleoside phosphorylase
PNP
EC 2.4.2.1
Inosine phosphorylase
PF01048 (PNP_UDP_1)
[Graphical View]
NP_000261.2 (Protein)
NM_000270.3 (DNA/RNA sequence)
P81989 Purine nucleoside phosphorylase
PNP
EC 2.4.2.1
Inosine phosphorylase
PF01048 (PNP_UDP_1)
[Graphical View]

KEGG enzyme name
purine-nucleoside phosphorylase
inosine phosphorylase
PNPase
PUNPI
PUNPII
inosine-guanosine phosphorylase
nucleotide phosphatase
purine deoxynucleoside phosphorylase
purine deoxyribonucleoside phosphorylase
purine nucleoside phosphorylase
purine ribonucleoside phosphorylase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P55859 PNPH_BOVIN Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate. Homotrimer.
P00491 PNPH_HUMAN Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate. Homotrimer.
P81989 PUNA_CELSP Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate. Homotrimer.

KEGG Pathways
Map code Pathways E.C.
MAP00230 Purine metabolism
MAP00240 Pyrimidine metabolism
MAP00760 Nicotinate and nicotinamide metabolism

Compound table
Substrates Products Intermediates
KEGG-id C15586 C00009 C15587 C00620
E.C.
Compound Purine nucleoside Orthophosphate Purine alpha-D-Ribose 1-phosphate
Type nucleoside phosphate group/phosphate ion aromatic ring (with nitrogen atoms) carbohydrate,phosphate group/phosphate ion
ChEBI 18255
26078
17258
35586
35588
35589
16300
PubChem 68368
1004
22486802
1044
439236
1a9oA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:PO4 Unbound Unbound
1a9pA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:9DI Bound:PO4 Unbound Unbound
1a9qA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:SO4 Bound:HPA Unbound
1a9rA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:SO4 Bound:HPA Unbound
1a9sA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:NOS Analogue:SO4 Unbound Unbound
1a9tA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:HPA Bound:R1P
1b8nA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:IMG Bound:PO4 Unbound Unbound
1b8oA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:IMH Bound:PO4 Unbound Unbound
1fxuA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:GU7 Bound:PO4 Unbound Unbound
1pbnA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1qe5A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:PO4 Unbound Unbound
1qe5B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:PO4 Unbound Unbound
1qe5C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:PO4 Unbound Unbound
1ulaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:SO4 Unbound Unbound
1ulbA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:SO4 Bound:GUN Unbound
1vfnA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:HPA Unbound
3pnpA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:PO4 Unbound Unbound
4pnpA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:PO4 Unbound Unbound
1c3xA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:PO4 Analogue:8IG Unbound
1c3xB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:PO4 Analogue:8IG Unbound
1c3xC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:PO4 Analogue:8IG Unbound

Reference for Active-site residues
resource references E.C.

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1a9oA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 201;ASN 243(Base binding);SER 33;HIS 64;ARG 84;HIS 86;SER 220(Phosphate);TYR 88;HIS 257(Ribose)
1a9pA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 201;ASN 243(Base binding);SER 33;HIS 64;ARG 84;HIS 86;SER 220(Phosphate);TYR 88;HIS 257(Ribose)
1a9qA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 201;ASN 243(Base binding);SER 33;HIS 64;ARG 84;HIS 86;SER 220(Phosphate);TYR 88;HIS 257(Ribose)
1a9rA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 201;ASN 243(Base binding);SER 33;HIS 64;ARG 84;HIS 86;SER 220(Phosphate);TYR 88;HIS 257(Ribose)
1a9sA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 201;ASN 243(Base binding);SER 33;HIS 64;ARG 84;HIS 86;SER 220(Phosphate);TYR 88;HIS 257(Ribose)
1a9tA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 201;ASN 243(Base binding);SER 33;HIS 64;ARG 84;HIS 86;SER 220(Phosphate);TYR 88;HIS 257(Ribose)
1b8nA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 201;ASN 243(Base binding);SER 33;HIS 64;ARG 84;HIS 86;SER 220(Phosphate);TYR 88;HIS 257(Ribose)
1b8oA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 201;ASN 243(Base binding);SER 33;HIS 64;ARG 84;HIS 86;SER 220(Phosphate);TYR 88;HIS 257(Ribose)
1fxuA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 201;ASN 243(Base binding);SER 33;HIS 64;ARG 84;HIS 86;SER 220(Phosphate);TYR 88;HIS 257(Ribose)
1pbnA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 201;ASN 243(Base binding);SER 33;HIS 64;ARG 84;HIS 86;SER 220(Phosphate);TYR 88;HIS 257(Ribose)
1qe5A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 204;ASN 246(Base binding);SER 46; ;ARG 103;HIS 105;SER 223(Phosphate);TYR 107;HIS 258(Ribose)
1qe5B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 204;ASN 246(Base binding);SER 46; ;ARG 103;HIS 105;SER 223(Phosphate);TYR 107;HIS 258(Ribose)
1qe5C Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 204;ASN 246(Base binding);SER 46; ;ARG 103;HIS 105;SER 223(Phosphate);TYR 107;HIS 258(Ribose)
1ulaA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 201;ASN 243(Base binding);SER 33;HIS 64;ARG 84;HIS 86;SER 220(Phosphate);TYR 88;HIS 257(Ribose)
1ulbA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 201;ASN 243(Base binding);SER 33;HIS 64;ARG 84;HIS 86;SER 220(Phosphate);TYR 88;HIS 257(Ribose)
1vfnA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 201;ASN 243(Base binding);SER 33; ;ARG 84;HIS 86;SER 220(Phosphate);TYR 88;HIS 257(Ribose)
3pnpA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 201;ASN 243(Base binding);SER 33;HIS 64;ARG 84;HIS 86;SER 220(Phosphate);TYR 88; (Ribose) invisible H257
4pnpA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 201;ASN 243(Base binding);SER 33;HIS 64;ARG 84;HIS 86;SER 220(Phosphate);TYR 88;HIS 257(Ribose)
1c3xA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 204;ASN 246(Base binding);SER 46; ;ARG 103;HIS 105;SER 223(Phosphate);TYR 107;HIS 258(Ribose)
1c3xB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 204;ASN 246(Base binding);SER 46; ;ARG 103;HIS 105;SER 223(Phosphate);TYR 107;HIS 258(Ribose)
1c3xC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 204;ASN 246(Base binding);SER 46; ;ARG 103;HIS 105;SER 223(Phosphate);TYR 107;HIS 258(Ribose)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[6]
Fig.7, Fig.9, p.11746-11747 3
[7]
Fig.8, p.7144-7145 2
[9]
Fig.5, p.1248-1250 3
[11]
Fig.1 2
[14]
Fig.5, Fig.7, p.14 2
[15]
Fig.1 2

References
[1]
Resource
Comments
Medline ID
PubMed ID 2104852
Journal J Biol Chem
Year 1990
Volume 265
Pages 1812-20
Authors Ealick SE, Rule SA, Carter DC, Greenhough TJ, Babu YS, Cook WJ, Habash J, Helliwell JR, Stoeckler JD, Parks RE Jr, et al
Title Three-dimensional structure of human erythrocytic purine nucleoside phosphorylase at 3.2 A resolution.
Related PDB
Related UniProtKB P00491
[2]
Resource
Comments
Medline ID
PubMed ID 1763067
Journal Proc Natl Acad Sci U S A
Year 1991
Volume 88
Pages 11540-4
Authors Ealick SE, Babu YS, Bugg CE, Erion MD, Guida WC, Montgomery JA, Secrist JA 3rd
Title Application of crystallographic and modeling methods in the design of purine nucleoside phosphorylase inhibitors.
Related PDB 1ula 1ulb
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 7607309
Journal FEBS Lett
Year 1995
Volume 367
Pages 214-8
Authors Bzowska A, Luic M, Schroder W, Shugar D, Saenger W, Koellner G
Title Calf spleen purine nucleoside phosphorylase: purification, sequence and crystal structure of its complex with an N(7)-acycloguanosine inhibitor.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 9020983
Journal J Mol Biol
Year 1997
Volume 265
Pages 202-16
Authors Koellner G, Luic M, Shugar D, Saenger W, Bzowska A
Title Crystal structure of calf spleen purine nucleoside phosphorylase in a complex with hypoxanthine at 2.15 A resolution.
Related PDB 1vfn
Related UniProtKB P55859
[5]
Resource
Comments
Medline ID
PubMed ID 9305962
Journal Biochemistry
Year 1997
Volume 36
Pages 11725-34
Authors Erion MD, Takabayashi K, Smith HB, Kessi J, Wagner S, Honger S, Shames SL, Ealick SE
Title Purine nucleoside phosphorylase. 1. Structure-function studies.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 9305963
Journal Biochemistry
Year 1997
Volume 36
Pages 11735-48
Authors Erion MD, Stoeckler JD, Guida WC, Walter RL, Ealick SE
Title Purine nucleoside phosphorylase. 2. Catalytic mechanism.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 9585525
Journal Biochemistry
Year 1998
Volume 37
Pages 7135-46
Authors Mao C, Cook WJ, Zhou M, Federov AA, Almo SC, Ealick SE
Title Calf spleen purine nucleoside phosphorylase complexed with substrates and substrate analogues.
Related PDB 1a9o 1a9p 1a9q 1a9r 1a9s 1a9t 1pbn
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 10404592
Journal Structure Fold Des
Year 1999
Volume 7
Pages 629-41
Authors Appleby TC, Erion MD, Ealick SE
Title The structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase at 1.7 A resolution provides insights into substrate binding and catalysis.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 10600382
Journal J Mol Biol
Year 1999
Volume 294
Pages 1239-55
Authors Tebbe J, Bzowska A, Wielgus-Kutrowska B, Schroder W, Kazimierczuk Z, Shugar D, Saenger W, Koellner G
Title Crystal structure of the purine nucleoside phosphorylase (PNP) from Cellulomonas sp. and its implication for the mechanism of trimeric PNPs.
Related PDB 1qe5 1c3x
Related UniProtKB P81989
[10]
Resource
Comments
Medline ID
PubMed ID 11134924
Journal Acta Crystallogr D Biol Crystallogr
Year 2001
Volume 57
Pages 30-6
Authors Luic M, Koellner G, Shugar D, Saenger W, Bzowska A
Title Calf spleen purine nucleoside phosphorylase: structure of its ternary complex with an N(7)-acycloguanosine inhibitor and a phosphate anion.
Related PDB 1fxu
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 11170405
Journal Biochemistry
Year 2001
Volume 40
Pages 853-60
Authors Fedorov A, Shi W, Kicska G, Fedorov E, Tyler PC, Furneaux RH, Hanson JC, Gainsford GJ, Larese JZ, Schramm VL, Almo SC
Title Transition state structure of purine nucleoside phosphorylase and principles of atomic motion in enzymatic catalysis.
Related PDB 1b8o 1b8n
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 11444966
Journal Biochemistry
Year 2001
Volume 40
Pages 8204-15
Authors Shi W, Basso LA, Santos DS, Tyler PC, Furneaux RH, Blanchard JS, Almo SC, Schramm VL
Title Structures of purine nucleoside phosphorylase from Mycobacterium tuberculosis in complexes with immucillin-H and its pieces.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 11591349
Journal Structure (Camb)
Year 2001
Volume 9
Pages 941-53
Authors Lee JE, Cornell KA, Riscoe MK, Howell PL
Title Structure of E. coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase reveals similarity to the purine nucleoside phosphorylases.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 11743878
Journal Biochem J
Year 2002
Volume 361
Pages 1-25
Authors Pugmire MJ, Ealick SE
Title Structural analyses reveal two distinct families of nucleoside phosphorylases.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 12463747
Journal Biochemistry
Year 2002
Volume 41
Pages 14489-98
Authors Kicska GA, Tyler PC, Evans GB, Furneaux RH, Shi W, Fedorov A, Lewandowicz A, Cahill SM, Almo SC, Schramm VL
Title Atomic dissection of the hydrogen bond network for transition-state analogue binding to purine nucleoside phosphorylase.
Related PDB
Related UniProtKB

Comments
The enzymes of this entry corresponds to the Trimeric subunit members of nucleoside phosphorylase family-I [14].
The literature [14] summarized the proposed catalytic mechanism of the enzyme. Beta-nucleoside binds in a high-energy (anticlinal torsion angle of the glycosidic bond, with the ribose moiety in the uncommon C-4'-endo sugar pucker), according to the literature [6]. This high-energy conformation produces steric strain, which induces glycosidic cleavage. The glycosidic bond is weakened further as electrons flow from O-4' of the ribose to the purine ring, resulting in an oxocarbenium ion that is stabilized by the negative charges of the phosphate ion. The phosphate ion binds on the alpha-side of the ribose ring, where it is postioned to participate in an SN1 nucleophilic attack at the C-1' position. The flow of electrons from the glycosidic bond to the purine ring is probably stabilized by active site residue (Asn) interactions at N-7 position of the purine base.

Created Updated
2002-07-12 2011-09-27