PDBsum entry: 1nw4

Transferase

PDB id: 1nw4

Contents

Protein chains

(+ 0 more) 243 a.a. *

Ligands

SO4 ×19

IMH ×6

IPA ×15

Waters ×248

* Residue conservation analysis

PDB id:

1nw4

Name:

Transferase

Title:

Crystal structure of plasmodium falciparum purine nucleoside phosphorylase in complex with immh and sulfate

Structure:

Uridine phosphorylase, putative. Chain: a, b, c, d, e, f. Engineered: yes

Source:

Plasmodium falciparum. Organism_taxid: 36329. Strain: 3d7. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Hexamer (from PQS)

Resolution:

2.20Å R-factor: 0.207 R-free: 0.248

Authors:

W.Shi,L.M.Ting,G.A.Kicska,A.Lewandowicz,P.C.Tyler,G.B.Evans, R.H.Furneaux,K.Kim,S.C.Almo,V.L.Schramm

Key ref:

W.Shi et al. (2004). Plasmodium falciparum purine nucleoside phosphorylase: crystal structures, immucillin inhibitors, and dual catalytic function. J Biol Chem, 279, 18103-18106. PubMed id: 14982926 DOI: 10.1074/jbc.C400068200

Date:

05-Feb-03 Release date: 16-Mar-04

Protein chains

Q8I3X4  (Q8I3X4_PLAF7) -  Purine nucleotide phosphorylase, putative

Seq: 245 a.a.

Struc: 243 a.a.

Enzyme reactions

• Enzyme class: E.C.2.4.2.3 - Uridine phosphorylase.
• Reaction: Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate

Uridine (Bound ligand (Het Group name = IMH) matches with 44.00% similarity) + phosphate = uracil + alpha-D-ribose 1-phosphate

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

 Gene Ontology (GO) functional annotation 

• Biological process: nucleoside metabolic process (1 term)
• Biochemical function: catalytic activity (4 terms)

reference

DOI no: 10.1074/jbc.C400068200

J Biol Chem 279:18103-18106 (2004)

PubMed id: 14982926

Plasmodium falciparum purine nucleoside phosphorylase: crystal structures, immucillin inhibitors, and dual catalytic function.

W.Shi, L.M.Ting, G.A.Kicska, A.Lewandowicz, P.C.Tyler, G.B.Evans, R.H.Furneaux, K.Kim, S.C.Almo, V.L.Schramm.

ABSTRACT

Purine nucleoside phosphorylase from Plasmodium falciparum (PfPNP) is an anti-malarial target based on the activity of Immucillins. The crystal structure of PfPNP.Immucillin-H (ImmH).SO(4) reveals a homohexamer with ImmH and SO(4) bound at each catalytic site. A solvent-filled cavity close to the 5'-hydroxyl group of ImmH suggested that PfPNP can accept additional functional groups at the 5'-carbon. Assays established 5'-methylthioinosine (MTI) as a substrate for PfPNP. MTI is not found in human metabolism. These properties of PfPNP suggest unusual purine pathways in P. falciparum and provide structural and mechanistic foundations for the design of malaria-specific transition state analogue inhibitors. 5'-Methylthio-Immucillin-H (MT-ImmH) was designed to resemble the transition state of PfPNP and binds to PfPNP and human-PNP with K(d) values of 2.7 and 303 nm, respectively, to give a discrimination factor of 112. MT-ImmH is the first inhibitor that favors PfPNP inhibition. The structure of PfPNP.MT-ImmH.SO(4) shows that the hydrophobic methylthio group inserts into a hydrophobic region adjacent to the more hydrophilic 5'-hydroxyl binding site of ImmH. The catalytic features of PfPNP indicate a dual cellular function in purine salvage and polyamine metabolism. Combined metabolic functions in a single enzyme strengthen the rationale for targeting PfPNP in anti-malarial action.

Selected figure(s)

Figure 2.
FIG. 2. X-ray crystal structure of PfPNP with ImmH and SO[4] at the catalytic sites. Panels show the hexamer (a) and stereo view of a single subunit (b). Panels were generated using SETOR (17).

Figure 3.
FIG. 3. Catalytic site contacts for ImmH and SO[4] at the catalytic sites of PfPNP (Protein Data Bank ID code 1NW4 [PDB] ) (a) compared with MT-ImmH and SO[4] in PfPNP (Protein Data Bank ID code 1Q1G [PDB] ) (b) and ImmH and PO[4] in bovine PNP (Protein Data Bank ID code 1B80 [PDB] ) (c). Amino acid residues labeled a in panels a and b are from the parent subunit, and those labeled b are from the neighbor subunit across the dimeric interface (see Fig. 2a). Distances are given in Angstroms. The lower panels are stereo views of electron density for the residues surrounding the catalytic sites of PfPNP (left) and human PNP (right). The stereo view of the channel in which the 5'-hydroxyl group of ImmH is bound is shown with the imino nitrogen of ImmH in blue and the 5'-hydroxyl oxygen in red (left). The oxygen points toward the viewer in a cavity of sufficient volume to accept a methylthio or homocysteine group. The cavity is filled with an isopropanol molecule from the solvent (shown in Fig. 4). Sulfate is bound in the cavity to the lower left and is yellow (S) and red (O). Human PNP·ImmH·PO[4] (right) has no open cavity (Protein Data Bank ID code 1RR6, unpublished observations). Electron density is a GRASP (18)-generated molecular surface for residues surrounding the catalytic site.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 18103-18106) copyright 2004.

Figures were selected by an automated process.