PDBsum entry 1a9o

Pentosyltransferase

PDB id: 1a9o

Contents

Protein chain

289 a.a. *

Ligands

PO4

Waters ×35

* Residue conservation analysis

PDB id:

1a9o

Name:

Pentosyltransferase

Title:

Bovine purine nucleoside phosphorylase complexed with phosphate

Structure:

Purine nucleoside phosphorylase. Chain: a. Ec: 2.4.2.1

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Organ: spleen

Biol. unit:

Trimer (from PQS)

Resolution:

2.00Å R-factor: 0.200

Authors:

C.Mao,W.J.Cook,M.Zhou,A.A.Fedorov,S.C.Almo,S.E.Ealick

Key ref:

C.Mao et al. (1998). Calf spleen purine nucleoside phosphorylase complexed with substrates and substrate analogues. Biochemistry, 37, 7135-7146. PubMed id: 9585525 DOI: 10.1021/bi9723919

Date:

10-Apr-98 Release date: 15-Jul-98

Protein chain

P55859  (PNPH_BOVIN) -  Purine nucleoside phosphorylase from Bos taurus

Seq: 289 a.a.

Struc: 289 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.4.2.1 - purine-nucleoside phosphorylase.
• Reaction:
  1. a purine D-ribonucleoside + phosphate = a purine nucleobase + alpha- D-ribose 1-phosphate
  2. a purine 2'-deoxy-D-ribonucleoside + phosphate = a purine nucleobase + 2-deoxy-alpha-D-ribose 1-phosphate

purine D-ribonucleoside + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly) = purine nucleobase + alpha- D-ribose 1-phosphate

purine 2'-deoxy-D-ribonucleoside + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly) = purine nucleobase + 2-deoxy-alpha-D-ribose 1-phosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi9723919

Biochemistry 37:7135-7146 (1998)

PubMed id: 9585525

Calf spleen purine nucleoside phosphorylase complexed with substrates and substrate analogues.

C.Mao, W.J.Cook, M.Zhou, A.A.Federov, S.C.Almo, S.E.Ealick.

ABSTRACT

Purine nucleoside phosphorylase (PNP) is a key enzyme in the purine salvage pathway, which provides an alternative to the de novo pathway for the biosynthesis of purine nucleotides. PNP catalyzes the reversible phosphorolysis of 2'-deoxypurine ribonucleosides to the free bases and 2-deoxyribose 1-phosphate. Absence of PNP activity in humans is associated with specific T-cell immune suppression. Its key role in these two processes has made PNP an important drug design target. We have investigated the structural details of the PNP-catalyzed reaction by determining the structures of bovine PNP complexes with various substrates and substrate analogues. The preparation of phosphate-free crystals of PNP has allowed us to analyze several novel complexes, including the ternary complex of PNP, purine base, and ribose 1-phosphate and of the completely unbound PNP. These results provide an atomic view for the catalytic mechanism for PNP proposed by M. D. Erion et al. [(1997) Biochemistry 36, 11735-11748], in which an oxocarbenium intermediate is stabilized by phosphate and the negative charge on the purine base is stabilized by active site residues. The bovine PNP structure reveals several new details of substrate and inhibitor binding, including two phosphate-induced conformational changes involving residues 33-36 and 56-69 and a previously undetected role for His64 in phosphate binding. In addition, a well-ordered water molecule is found in the PNP active site when purine base or nucleoside is also present. In contrast to human PNP, only one phosphate binding site was observed. Although binary complexes were observed for nucleoside, purine base, or phosphate, ribose 1-phosphate binding occurs only in the presence of purine base.