PDBsum entry 1php

Kinase

PDB id: 1php

Contents

Protein chain

394 a.a. *

Ligands

ADP

Metals

_MG

Waters ×634

* Residue conservation analysis

PDB id:

1php

Name:

Kinase

Title:

Structure of the adp complex of the 3-phosphoglycerate kinase from bacillus stearothermophilus at 1.65 angstroms

Structure:

3-phosphoglycerate kinase. Chain: a. Engineered: yes

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422

Resolution:

1.65Å R-factor: 0.156

Authors:

G.J.Davies,H.C.Watson

Key ref:

G.J.Davies et al. (1994). Structure of the ADP complex of the 3-phosphoglycerate kinase from Bacillus stearothermophilus at 1.65 A. Acta Crystallogr D Biol Crystallogr, 50, 202-209. PubMed id: 15299460 DOI: 10.1107/S0907444993011138

Date:

12-Apr-94 Release date: 22-Jun-94

Protein chain

P18912  (PGK_GEOSE) -  Phosphoglycerate kinase from Geobacillus stearothermophilus

Seq: 394 a.a.

Struc: 394 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.2.3 - phosphoglycerate kinase.
• Pathway: Calvin Cycle (carbon fixation stages)
• Reaction: (2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP

(2R)-3-phosphoglycerate + ATP = (2R)-3-phospho-glyceroyl phosphate + ADP (Bound ligand (Het Group name = ADP) corresponds exactly)

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

Added reference

DOI no: 10.1107/S0907444993011138

Acta Crystallogr D Biol Crystallogr 50:202-209 (1994)

PubMed id: 15299460

Structure of the ADP complex of the 3-phosphoglycerate kinase from Bacillus stearothermophilus at 1.65 A.

G.J.Davies, S.J.Gamblin, J.A.Littlechild, Z.Dauter, K.S.Wilson, H.C.Watson.

ABSTRACT

The structure of the ADP complex of the enzyme 3-phosphoglycerate kinase (PGK, E.C. 2.7.2.3) from Bacillus stearothermophilus NCA-1503 has been determined by the method of molecular replacement. The structure has been refined to an R factor of 0.16 for all data between 10.0 and 1.65 A resolution, using data collected on the Hendrix-Lentfer imaging plate at the EMBL outstation in Hamburg. The r.m.s. deviations from stereochemical ideality are 0.010 and 0.011 A for bonds and planes, respectively. Although crystallized in the presence of the nucleotide product MgATP, the high-resolution structure reveals the bound nucleotide to be MgADP reflecting the low intrinsic ATPase activity of PGK. Although the two domains of this enzyme are found to be some 4.5 degrees closer together than is found in the yeast and horse-muscle apo-enzyme structures, this structure represents the 'open' rather than the 'closed', catalytically competent form, of the enzyme.

Selected figure(s)

Figure 1.
Fig. 1. Ribbon diagram, drawn with the MOLSCRIPTprogram (Kraulis, 1990), howing the structure of B. stearothermophilus PGK. The nu- cleotide substrate atos are shown in 'ball-and-stck' representatin. Te 3-PGA site, on the N-terminal domain, as detemined by Harlos, Vas & Blake (1992) for the pig-muscle enzyme, is indicated.

Figure 9.
Fig. 9. Schematic diagram illustratig the main interactions of the nucleotide substrate, ADP, with the enzyme.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1994, 50, 202-209) copyright 1994.

Figures were selected by an automated process.