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PDBsum entry 1vjc

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protein ligands metals links
Transferase PDB id
1vjc
Jmol
Contents
Protein chain
416 a.a. *
Ligands
ATP
Metals
_MG
Waters ×185
* Residue conservation analysis
PDB id:
1vjc
Name: Transferase
Title: Structure of pig muscle pgk complexed with mgatp
Structure: Phosphoglycerate kinase. Chain: a. Ec: 2.7.2.3
Source: Sus scrofa. Pig. Organism_taxid: 9823. Tissue: muscle
Resolution:
2.10Å     R-factor:   0.173     R-free:   0.233
Authors: B.Flachner,Z.Kovari,A.Varga,Z.Gugolya,F.Vonderviszt,G.Naray- Szabo,M.Vas
Key ref:
B.Flachner et al. (2004). Role of phosphate chain mobility of MgATP in completing the 3-phosphoglycerate kinase catalytic site: binding, kinetic, and crystallographic studies with ATP and MgATP. Biochemistry, 43, 3436-3449. PubMed id: 15035615 DOI: 10.1021/bi035022n
Date:
03-Feb-04     Release date:   30-Mar-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q7SIB7  (PGK1_PIG) -  Phosphoglycerate kinase 1
Seq:
Struc:
417 a.a.
416 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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
Bound ligand (Het Group name = ATP)
corresponds exactly
+ 3-phospho-D-glycerate
= ADP
+ 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: 10.1021/bi035022n Biochemistry 43:3436-3449 (2004)
PubMed id: 15035615  
 
 
Role of phosphate chain mobility of MgATP in completing the 3-phosphoglycerate kinase catalytic site: binding, kinetic, and crystallographic studies with ATP and MgATP.
B.Flachner, Z.Kovári, A.Varga, Z.Gugolya, F.Vonderviszt, G.Náray-Szabó, M.Vas.
 
  ABSTRACT  
 
The complexes of pig muscle 3-phosphoglycerate kinase with the substrate MgATP and with the nonsubstrate Mg(2+)-free ATP have been characterized by binding, kinetic, and crystallographic studies. Comparative experiments with ADP and MgADP have also been carried out. In contrast to the less specific and largely ionic binding of Mg(2+)-free ATP and ADP, specific occupation of the adenosine binding pocket by MgATP and MgADP has been revealed by displacement experiments with adenosine and anions, as well as supported by isothermal calorimetric titrations. The Mg(2+)-free nucleotides similarly stabilize the overall protein structure and restrict the conformational flexibility around the reactive thiol groups of helix 13, as observed by differential scanning microcalorimetry and thiol reactivity studies, respectively. The metal complexes, however, behave differently. MgADP, but not MgATP, further increases the conformational stability with respect to its Mg(2+)-free form, which indicates their different modes of binding to the enzyme. Crystal structures of the binary complexes of the enzyme with MgATP and with ATP (2.1 and 1.9 A resolution, respectively) have shown that the orientation and interaction of phosphates of MgATP largely differ not only from those of ATP but also from the previously determined ones of either MgADP [Davies, G. J., Gamblin, S. J., Littlechild, J. A., Dauter, Z., Wilson, K. S., and Watson, H. C. (1994) Acta Crystallogr. D50, 202-209] or the metal complexes of AMP-PNP [May, A., Vas, M., Harlos, K., and Blake, C. C. F. (1996) Proteins 24, 292-303; Auerbach, G., Huber, R., Grattinger, M., Zaiss, K., Schurig, H., Jaenicke, R., and Jacob, U. (1997) Structure 5, 1475-1483] and are more similar to the interactions formed with MgAMP-PCP [Kovári, Z., Flachner, B., Náray-Szabó, G., and Vas, M. (2002) Biochemistry 41, 8796-8806]. Mg(2+) is liganded to both beta- and gamma-phosphates of ATP, while beta-phosphate is linked to the conserved Asp218, i.e., to the N-terminus of helix 8, through a water molecule; the known interactions of either MgADP or the metal complexes of AMP-PNP with the N-terminus of helix 13 and with Asn336 of beta-strand J are absent in the case of MgATP. Fluctuation of MgATP phosphates between two alternative sites has been proposed to facilitate the correct positioning of the mobile side chain of Lys215, and the catalytically competent active site is thereby completed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19016839 A.R.Mattoo, A.Arora, S.Maiti, and Y.Singh (2008).
Identification, characterization and activation mechanism of a tyrosine kinase of Bacillus anthracis.
  FEBS J, 275, 6237-6247.  
18190531 A.R.Mattoo, M.Saif Zaman, G.P.Dubey, A.Arora, A.Narayan, N.Jailkhani, K.Rathore, S.Maiti, and Y.Singh (2008).
Spo0B of Bacillus anthracis - a protein with pleiotropic functions.
  FEBS J, 275, 739-752.  
18463139 C.Gondeau, L.Chaloin, P.Lallemand, B.Roy, C.Périgaud, T.Barman, A.Varga, M.Vas, C.Lionne, and S.T.Arold (2008).
Molecular basis for the lack of enantioselectivity of human 3-phosphoglycerate kinase.
  Nucleic Acids Res, 36, 3620-3629.
PDB codes: 2zgv 3c39 3c3a 3c3b 3c3c
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
17222195 E.Beutler (2007).
PGK deficiency.
  Br J Haematol, 136, 3.  
16220545 A.Ababou, and J.E.Ladbury (2006).
Survey of the year 2004: literature on applications of isothermal titration calorimetry.
  J Mol Recognit, 19, 79-89.  
16740138 J.M.Flanagan, M.Rhodes, M.Wilson, and E.Beutler (2006).
The identification of a recurrent phosphoglycerate kinase mutation associated with chronic haemolytic anaemia and neurological dysfunction in a family from USA.
  Br J Haematol, 134, 233-237.  
16043694 A.L.Buchachenko, D.A.Kouznetsov, M.A.Orlova, and A.A.Markarian (2005).
Magnetic isotope effect of magnesium in phosphoglycerate kinase phosphorylation.
  Proc Natl Acad Sci U S A, 102, 10793-10796.  
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.  
16172677 H.Sigel, and R.Griesser (2005).
Nucleoside 5'-triphosphates: self-association, acid-base, and metal ion-binding properties in solution.
  Chem Soc Rev, 34, 875-900.  
15208312 O.Barabás, V.Pongrácz, J.Kovári, M.Wilmanns, and B.G.Vértessy (2004).
Structural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase.
  J Biol Chem, 279, 42907-42915.
PDB codes: 1rn8 1rnj 1seh 1syl
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.