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Phosphotransferase (carboxyl acceptor) PDB id
1qpg
Jmol
Contents
Protein chain
415 a.a. *
Ligands
MAP
3PG
Waters ×82
* Residue conservation analysis
PDB id:
1qpg
Name: Phosphotransferase (carboxyl acceptor)
Title: 3-phosphoglycerate kinase, mutation r65q
Structure: 3-phosphoglycerate kinase. Chain: a. Synonym: pgk. Engineered: yes. Mutation: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.
Biol. unit: Dimer (from PQS)
Resolution:
2.40Å     R-factor:   0.185    
Authors: T.M.Mcphillips,B.T.Hsu,M.A.Sherman,M.T.Mas,D.C.Rees
Key ref:
T.M.McPhillips et al. (1996). Structure of the R65Q mutant of yeast 3-phosphoglycerate kinase complexed with Mg-AMP-PNP and 3-phospho-D-glycerate. Biochemistry, 35, 4118-4127. PubMed id: 8672447 DOI: 10.1021/bi952500o
Date:
04-Jan-96     Release date:   10-Jun-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00560  (PGK_YEAST) -  Phosphoglycerate kinase
Seq:
Struc: 		416 a.a.
415 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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
Bound ligand (Het Group name = 3PG)
corresponds exactly 		=
ADP
Bound ligand (Het Group name = MAP)
matches with 78.00% similarity 		+ 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   3 terms 
  Biological process     gluconeogenesis   2 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi952500o Biochemistry 35:4118-4127 (1996)
PubMed id: 8672447  
 
 
Structure of the R65Q mutant of yeast 3-phosphoglycerate kinase complexed with Mg-AMP-PNP and 3-phospho-D-glycerate.
T.M.McPhillips, B.T.Hsu, M.A.Sherman, M.T.Mas, D.C.Rees.
 
  ABSTRACT  
 
The structure of a ternary complex of the R65Q mutant of yeast 3-phosphoglycerate kinase (PGK) with magnesium 5'-adenylylimidodiphosphate (Mg-AMP-PNP) and 3-phospho-D-glycerate (3-PG) has been determined by X-ray crystallography to 2.4 angstrom resolution. The structure was solved by single isomorphous replacement, anamalous scattering, and solvent flattening and has been refined to an R-factor of 0.185, with rms deviations from ideal bond distance and angles of 0.009 angstrom and 1.78 degrees, respectively. PGK consists of two domains, with the 3-PG bound to a "basic patch" of residues from the N-terminal domain and the Mg-AMP-PNP interacting with residues from the C-terminal domain. The two ligands are separated by approximately 11 angstrom across the interdomain cleft. The model of the R65Q mutant of yeast PGK is very similar to the structures of PGK isolated from horse, pig, and Bacillus stearothermophilus (rms deviations between equivalent alpha-carbons in the individual domains < 1.0 angstrom) but exhibits substantial variations with a previously reported yeast structure (rms deviations between equivalent alpha-carbons in the individual domains of 2.9-3.2 angstrom). The most significant tertiary structural differences among the yeast R65Q, equine, porcine, and B. stearothermophilus PGK structures occur in the relative orientations of the two domains. However, the relationships between the observed conformations of PGK are inconsistent with a "hinge-bending" behavior that would close the interdomain cleft. It is proposed that the available structural and biochemical data on PGK may indicate that the basic patch primarily represents the site of anion activation and not the catalytically active binding site for 3-PG.
 

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.  
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.  
16034819 J.R.de Almeida, L.M.de Moraes, and F.A.Torres (2005).
Molecular characterization of the 3-phosphoglycerate kinase gene (PGK1) from the methylotrophic yeast Pichia pastoris.
  Yeast, 22, 725-737.  
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.  
12454459 P.Tougard, T.Bizebard, M.Ritco-Vonsovici, P.Minard, and M.Desmadril (2002).
Structure of a circularly permuted phosphoglycerate kinase.
  Acta Crystallogr D Biol Crystallogr, 58, 2018-2023.
PDB code: 1fw8
11114510 H.Erlandsen, E.E.Abola, and R.C.Stevens (2000).
Combining structural genomics and enzymology: completing the picture in metabolic pathways and enzyme active sites.
  Curr Opin Struct Biol, 10, 719-730.  
  10593256 S.Kumar, B.Ma, C.J.Tsai, H.Wolfson, and R.Nussinov (1999).
Folding funnels and conformational transitions via hinge-bending motions.
  Cell Biochem Biophys, 31, 141-164.  
9622507 A.N.Szilágyi, and M.Vas (1998).
Anion activation of 3-phosphoglycerate kinase requires domain closure.
  Biochemistry, 37, 8551-8563.  
  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.  
9744480 C.Valentin, H.Birgens, C.T.Craescu, K.Brødum-Nielsen, and M.Cohen-Solal (1998).
A phosphoglycerate kinase mutant (PGK Herlev; D285V) in a Danish patient with isolated chronic hemolytic anemia: mechanism of mutation and structure-function relationships.
  Hum Mutat, 12, 280-287.  
9548916 L.M.Lester, L.A.Rusch, G.J.Robinson, and D.C.Speckhard (1998).
Mapping the active sites of 3-phosphoglycerate kinase and glycerol kinase with monoammine chromium(III) ATP.
  Biochemistry, 37, 5349-5355.  
9154937 A.Geerlof, P.P.Schmidt, F.Travers, and T.Barman (1997).
Cryoenzymic studies on yeast 3-phosphoglycerate kinase. Attempt to obtain the kinetics of the hinge-bending motion.
  Biochemistry, 36, 5538-5545.  
  9384563 G.Auerbach, R.Huber, M.Grättinger, K.Zaiss, H.Schurig, R.Jaenicke, and U.Jacob (1997).
Closed structure of phosphoglycerate kinase from Thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability.
  Structure, 5, 1475-1483.
PDB code: 1vpe
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.  
  9165087 L.Prade, P.Hof, and B.Bieseler (1997).
Dimer interface of glutathione S-transferase from Arabidopsis thaliana: influence of the G-site architecture on the dimer interface and implications for classification.
  Biol Chem, 378, 317-320.  
  9098898 M.A.Sherman, Y.Chen, and M.T.Mas (1997).
An engineered amino-terminal domain of yeast phosphoglycerate kinase with native-like structure.
  Protein Sci, 6, 882-891.  
9129831 N.Murali, Y.Lin, Y.Mechulam, P.Plateau, and B.D.Rao (1997).
Adenosine conformations of nucleotides bound to methionyl tRNA synthetase by transferred nuclear Overhauser effect spectroscopy.
  Biophys J, 72, 2275-2284.  
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 code is shown on the right.