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PDBsum entry 1php

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protein ligands metals links
Kinase PDB id
1php
Jmol
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P18912  (PGK_GEOSE) -  Phosphoglycerate kinase
Seq:
Struc:
394 a.a.
394 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.7.2.3  - Phosphoglycerate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Calvin Cycle (carbon fixation stages)
      Reaction: ATP + 3-phospho-D-glycerate = ADP + 3-phospho-D-glyceroyl phosphate
ATP
+ 3-phospho-D-glycerate
=
ADP
Bound ligand (Het Group name = ADP)
corresponds exactly
+ 3-phospho-D-glyceroyl phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     phosphorylation   2 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20065119 G.B.Gloor, G.Tyagi, D.M.Abrassart, A.J.Kingston, A.D.Fernandes, S.D.Dunn, and C.J.Brandl (2010).
Functionally compensating coevolving positions are neither homoplasic nor conserved in clades.
  Mol Biol Evol, 27, 1181-1191.  
19292872 R.Encalada, A.Rojo-Domínguez, J.S.Rodríguez-Zavala, J.P.Pardo, H.Quezada, R.Moreno-Sánchez, and E.Saavedra (2009).
Molecular basis of the unusual catalytic preference for GDP/GTP in Entamoeba histolytica 3-phosphoglycerate kinase.
  FEBS J, 276, 2037-2047.  
18004764 G.M.Sawyer, A.F.Monzingo, E.C.Poteet, D.A.O'Brien, and J.D.Robertus (2008).
X-ray analysis of phosphoglycerate kinase 2, a sperm-specific isoform from Mus musculus.
  Proteins, 71, 1134-1144.
PDB codes: 2p9q 2p9t 2paa
17158564 E.Balog, M.Laberge, and J.Fidy (2007).
The influence of interdomain interactions on the intradomain motions in yeast phosphoglycerate kinase: a molecular dynamics study.
  Biophys J, 92, 1709-1716.  
17206660 J.T.Huang, J.P.Cheng, and H.Chen (2007).
Secondary structure length as a determinant of folding rate of proteins with two- and three-state kinetics.
  Proteins, 67, 12-17.  
15819882 A.Varga, B.Flachner, E.Gráczer, S.Osváth, A.N.Szilágyi, and M.Vas (2005).
Correlation between conformational stability of the ternary enzyme-substrate complex and domain closure of 3-phosphoglycerate kinase.
  FEBS J, 272, 1867-1885.  
16227206 L.Zecchinon, A.Oriol, U.Netzel, J.Svennberg, N.Gerardin-Otthiers, and G.Feller (2005).
Stability domains, substrate-induced conformational changes, and hinge-bending motions in a psychrophilic phosphoglycerate kinase. A microcalorimetric study.
  J Biol Chem, 280, 41307-41314.  
12509431 D.L.Jakeman, A.J.Ivory, G.M.Blackburn, and M.P.Williamson (2003).
Orientation of 1,3-bisphosphoglycerate analogs bound to phosphoglycerate kinase.
  J Biol Chem, 278, 10957-10962.  
11782484 A.J.Lay, X.M.Jiang, E.Daly, L.Sun, and P.J.Hogg (2002).
Plasmin reduction by phosphoglycerate kinase is a thiol-independent process.
  J Biol Chem, 277, 9062-9068.  
11248706 A.N.Szilágyi, N.V.Kotova, G.V.Semisotnov, and M.Vas (2001).
Incomplete refolding of a fragment of the N-terminal domain of pig muscle 3-phosphoglycerate kinase that lacks a subdomain. Comparison with refolding of the complementary C-terminal fragment.
  Eur J Biochem, 268, 1851-1860.  
10753921 M.Bentahir, G.Feller, M.Aittaleb, J.Lamotte-Brasseur, T.Himri, J.P.Chessa, and C.Gerday (2000).
Structural, kinetic, and calorimetric characterization of the cold-active phosphoglycerate kinase from the antarctic Pseudomonas sp. TACII18.
  J Biol Chem, 275, 11147-11153.  
10092885 J.McHarg, S.M.Kelly, N.C.Price, A.Cooper, and J.A.Littlechild (1999).
Site-directed mutagenesis of proline 204 in the 'hinge' region of yeast phosphoglycerate kinase.
  Eur J Biochem, 259, 939-945.  
  9521128 B.E.Bernstein, P.A.Michels, H.Kim, P.H.Petra, and W.G.Hol (1998).
The importance of dynamic light scattering in obtaining multiple crystal forms of Trypanosoma brucei PGK.
  Protein Sci, 7, 504-507.  
9017217 K.M.Pappu, B.Kunnumal, and E.H.Serpersu (1997).
A new metal-binding site for yeast phosphoglycerate kinase as determined by the use of a metal-ATP analog.
  Biophys J, 72, 928-935.  
8785318 C.A.Smith, and I.Rayment (1996).
Active site comparisons highlight structural similarities between myosin and other P-loop proteins.
  Biophys J, 70, 1590-1602.  
8521845 C.E.Jones, T.M.Fleming, D.A.Cowan, J.A.Littlechild, and P.W.Piper (1995).
The phosphoglycerate kinase and glyceraldehyde-3-phosphate dehydrogenase genes from the thermophilic archaeon Sulfolobus solfataricus overlap by 8-bp. Isolation, sequencing of the genes and expression in Escherichia coli.
  Eur J Biochem, 233, 800-808.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.