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PDBsum entry 2ie8

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protein links
Transferase PDB id
2ie8
Jmol
Contents
Protein chain
390 a.a. *
Waters ×152
* Residue conservation analysis
PDB id:
2ie8
Name: Transferase
Title: Crystal structure of thermus caldophilus phosphoglycerate kinase in the open conformation
Structure: Phosphoglycerate kinase. Chain: a. Engineered: yes
Source: Thermus caldophilus. Organism_taxid: 272. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.80Å     R-factor:   0.201     R-free:   0.273
Authors: J.H.Lee,Y.J.Im,S.H.Eom
Key ref: J.H.Lee et al. (2006). Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation. Biochem Biophys Res Commun, 350, 1044-1049. PubMed id: 17045964 DOI: 10.1016/j.bbrc.2006.09.151
Date:
18-Sep-06     Release date:   07-Nov-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q08GC7  (Q08GC7_THECA) -  Phosphoglycerate kinase
Seq:
Struc:
390 a.a.
390 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
+ 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: 10.1016/j.bbrc.2006.09.151 Biochem Biophys Res Commun 350:1044-1049 (2006)
PubMed id: 17045964  
 
 
Crystal structure of Thermus caldophilus phosphoglycerate kinase in the open conformation.
J.H.Lee, Y.J.Im, J.Bae, D.Kim, M.K.Kim, G.B.Kang, D.S.Lee, S.H.Eom.
 
  ABSTRACT  
 
Phosphoglycerate kinase (PGK) is a key glycolytic enzyme that catalyzes the reversible transfer of a phosphate from 1,3-bisphosphoglycerate to ADP to form 3-phosphoglycerate and ATP in the presence of magnesium. During catalysis, a conformational change occurs that brings the N- and C-domains of PGK closer together. Here we present the 1.8A crystal structure of unliganded PGK from Thermus caldophilus (Tca). Comparison of the structure of TcaPGK (open conformation) with that of Thermotoga maritima (Tma) PGK (closed conformation) revealed that the conformational change reflects a change in the interaction between the domains. We identified Arg148 as a key residue involved in open-to-closed transition. The open conformation of TcaPGK is stabilized by an interdomain salt bridge between Arg148 and Glu375. The binding of 3-PG (or maybe 1,3-BPG) disrupts this salt bridge and, in ternary complex, the formation of new salt bridge between Arg60 and Asp197 stabilizes the closed conformation.
 

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.  
18318710 A.E.Andrade, L.P.Silva, J.L.Pereira, E.F.Noronha, F.B.Reis, C.Bloch, M.F.dos Santos, G.B.Domont, O.L.Franco, and A.Mehta (2008).
In vivo proteome analysis of Xanthomonas campestris pv. campestris in the interaction with the host plant Brassica oleracea.
  FEMS Microbiol Lett, 281, 167-174.  
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
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.