PDBsum entry 1vfn

Nucleoside phosphorylase

PDB id: 1vfn

Contents

Protein chain

270 a.a. *

Ligands

HPA

Metals

_MG

_ZN

Waters ×129

* Residue conservation analysis

PDB id:

1vfn

Name:

Nucleoside phosphorylase

Title:

Purine nucleoside phosphorylase

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:

2.15Å R-factor: 0.180

Authors:

G.Koellner,A.Bzowska

Key ref:

G.Koellner et al. (1997). Crystal structure of calf spleen purine nucleoside phosphorylase in a complex with hypoxanthine at 2.15 A resolution. J Mol Biol, 265, 202-216. PubMed id: 9020983 DOI: 10.1006/jmbi.1996.0730

Date:

08-Oct-96 Release date: 12-Nov-97

Protein chain

P55859  (PNPH_BOVIN) -  Purine nucleoside phosphorylase from Bos taurus

Seq: 289 a.a.

Struc: 270 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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

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

reference

DOI no: 10.1006/jmbi.1996.0730

J Mol Biol 265:202-216 (1997)

PubMed id: 9020983

Crystal structure of calf spleen purine nucleoside phosphorylase in a complex with hypoxanthine at 2.15 A resolution.

G.Koellner, M.Luić, D.Shugar, W.Saenger, A.Bzowska.

ABSTRACT

Trimeric calf spleen purine nucleoside phosphorylase has been complexed with hypoxanthine via phosphorolysis of inosine in the presence of phosphate. The resulting, "Michaelis" complex (three hypoxanthine molecules per trimer), presumed to be formed under these conditions, crystallized in the cubic space group P2(1)3, with unit cell dimension a = 94.11 A and one monomer in the asymmetric crystal unit; the biologically active trimer is located on the crystallographic 3-fold axis. High-resolution X-ray diffraction data were collected using synchrotron radiation (EMBL outstation, Hamburg, c/o DESY). The crystal structure has been determined by molecular replacement and refined at 2.15 A resolution to an R-value of 0.18. In the hypoxanthine binding site, a cis-peptide bond between Asn243 and Lys244 is observed. Side-chains of GIu201 and Asn243, as well as one integral water molecule located in the base binding site, form hydrogen bonds with the hypoxanthine N-1 H, N-7 H and O-6. A second water molecule links the base positions N-3 and N-9 with an adjacent pocket, which presumably is the phosphate-binding site. This pocket is filled completely by a cluster of six water molecules. Hence all possible donor/acceptor-positions of hypoxanthine are saturated by hydrogen-bonding to protein side-chains or integral water molecules. Purine nucleoside phosphorylase isolated form human tissues is a primary target for chemotherapeutic intervention, and the more stable calf enzyme has similar physico-chemical and kinetic properties, as well as response to inhibitors. Hence the high-resolution structure presented here may serve for design of inhibitors with potential pharmacological applications.

Selected figure(s)

Figure 4.
Figure 4. Mode of binding of the unidentified metal cation (see the text and Figure 1) located on the 3-fold axis. The cation is coordinated by His20 N^ epsilon of three symmetry-related trimers and water molecules Wat429 and Wat430. Hydrogen bond lengths are denoted in Å (drawn with SCHAKAL; [Keller 1988]).

Figure 5.
Figure 5. A drawing of the trimeric calf spleen PNP-Hx complex. The location of the unidentified metal cation (see also Figure 2 and Figure 4) is shown as a circle with enlarged van der Waals radius in each monomer. Direct contacts between monomers forming the trimer are mainly from the loop between residues 141 and 168 of one monomer, which is the longest loop belting the monomer from one side (in red, see also (Table 4 and Table 4)). Drawn with MOLSCRIPT [Kraulis 1991].

The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 265, 202-216) copyright 1997.

Figures were selected by an automated process.