Purine nucleoside phosphorylase DeoD-type

 

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

 

Reference Protein and Structure

Sequence
P0ABP8 UniProt (2.4.2.1) IPR004402 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
4ts9 - Crystal structure of wild type E. Coli purine nucleoside phosphorylase with 6 FMC molecules (1.77 Å) PDBe PDBsum 4ts9
Catalytic CATH Domains
3.40.50.1580 CATHdb (see all for 4ts9)
Click To Show Structure

Enzyme Reaction (EC:2.4.2.1)

inosine
CHEBI:17596ChEBI
+
hydrogenphosphate
CHEBI:43474ChEBI
→
alpha-D-ribose 1-phosphate(2-)
CHEBI:57720ChEBI
+
hypoxanthine
CHEBI:17368ChEBI
Alternative enzyme names: PNPase, PUNPI, PUNPII, Inosine phosphorylase, Inosine-guanosine phosphorylase, Nucleotide phosphatase, Purine deoxynucleoside phosphorylase, Purine deoxyribonucleoside phosphorylase, Purine nucleoside phosphorylase, Purine ribonucleoside phosphorylase,

Enzyme Mechanism

Introduction

Catalytic action involves protonation of the purine base at position N7 by the side-chain of Asp204, which is initially in the acid form. The proton transfer is triggered by the Arg217 side-chain which is moved by the conformation change into hydrogen bond distance to Asp204. When the substrate is protonated, it can be attacked by the negatively charged orthophosphate group.

Catalytic Residues Roles

UniProt PDB* (4ts9)
Asp205 Asp204A Transfers a proton to the substrate, activating it for attack. proton shuttle (general acid/base)
Gly21 (main-N), Ser91 (main-N), Arg44, Arg25, Arg88 Gly20A (main-N), Ser90A (main-N), Arg43C, Arg24A, Arg87A Help stabilise the negative charge build-up in the active site. electrostatic stabiliser
Arg218 Arg217A Triggers proton transfer from Asp204 to the substrate. enhance reactivity
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

References

  1. Koellner G et al. (2002), J Mol Biol, 315, 351-371. Open and closed conformation of the E. coli purine nucleoside phosphorylase active center and implications for the catalytic mechanism. DOI:10.1006/jmbi.2001.5211. PMID:11786017.

Step 1.

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Catalytic Residues Roles

Residue Roles
Arg217A enhance reactivity
Asp204A proton shuttle (general acid/base)
Gly20A (main-N) electrostatic stabiliser
Arg24A electrostatic stabiliser
Arg87A electrostatic stabiliser
Ser90A (main-N) electrostatic stabiliser
Arg43C electrostatic stabiliser

Chemical Components

Step 1.

Contributors

James W. Murray, Craig Porter, Gemma L. Holliday