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PDBsum entry 2akz

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protein ligands metals Protein-protein interface(s) links
Lyase PDB id
2akz
Jmol
Contents
Protein chains
435 a.a. *
Ligands
PO4 ×2
TRS
Metals
__F ×4
_MG ×4
Waters ×967
* Residue conservation analysis
PDB id:
2akz
Name: Lyase
Title: Fluoride inhibition of enolase: crystal structure of the inhibitory complex
Structure: Gamma enolase. Chain: a, b. Synonym: 2-phospho-d-glycerate hydro-lyase. Neural enolase. Neuron-specific enolase. Nse. Enolase 2. Engineered: yes. Other_details: inhibitory complex
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: eno2. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
1.36Å     R-factor:   0.121     R-free:   0.144
Authors: J.Qin,G.Chai,J.M.Brewer,L.L.Lovelace
Key ref:
J.Qin et al. (2006). Fluoride inhibition of enolase: crystal structure and thermodynamics. Biochemistry, 45, 793-800. PubMed id: 16411755 DOI: 10.1021/bi051558s
Date:
04-Aug-05     Release date:   21-Mar-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P09104  (ENOG_HUMAN) -  Gamma-enolase
Seq:
Struc:
434 a.a.
435 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.11  - Phosphopyruvate hydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O
2-phospho-D-glycerate
=
phosphoenolpyruvate
Bound ligand (Het Group name = PO4)
matches with 50.00% similarity
+ H(2)O
      Cofactor: Mg(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     photoreceptor inner segment   11 terms 
  Biological process     small molecule metabolic process   5 terms 
  Biochemical function     lyase activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi051558s Biochemistry 45:793-800 (2006)
PubMed id: 16411755  
 
 
Fluoride inhibition of enolase: crystal structure and thermodynamics.
J.Qin, G.Chai, J.M.Brewer, L.L.Lovelace, L.Lebioda.
 
  ABSTRACT  
 
Enolase is a dimeric metal-activated metalloenzyme which uses two magnesium ions per subunit: the strongly bound conformational ion and the catalytic ion that binds to the enzyme-substrate complex inducing catalysis. The crystal structure of the human neuronal enolase-Mg2F2P(i) complex (enolase fluoride/phosphate inhibitory complex, EFPIC) determined at 1.36 A resolution shows that the combination of anions effectively mimics an intermediate state in catalysis. The phosphate ion binds in the same site as the phosphate group of the substrate/product, 2-phospho-D-glycerate/phosphoenolpyruvate, and induces binding of the catalytic Mg2+ ion. One fluoride ion bridges the structural and catalytic magnesium ions while the other interacts with the structural magnesium ion and the ammonio groups of Lys 342 and Lys 393. These fluoride ion positions correspond closely to the positions of the oxygen atoms of the substrate's carboxylate moiety. To relate structural changes resulting from fluoride, phosphate, and magnesium ions binding to those that are induced by phosphate and magnesium ions alone, we also determined the structure of the human neuronal enolase-Mg2P(i) complex (enolase phosphate inhibitory complex, EPIC) at 1.92 A resolution. It shows the closed conformation in one subunit and a mixture of open and semiclosed conformations in the other. The EPFIC dimer is essentially symmetric while the EPIC dimer is asymmetric. Isothermal titration calorimetry data confirmed binding of four fluoride ions per dimer and yielded Kb values of 7.5 x 10(5) +/- 1.3 x 10(5), 1.2 x 10(5) +/- 0.2 x 10(5), 8.6 x 10(4) +/- 1.6 x 10(4), and 1.6 x 10(4) +/- 0.7 x 10(4) M(-1). The different binding constants indicate negative cooperativity between the subunits; the asymmetry of EPIC supports such an interpretation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18200608 O.Okhrimenko, and I.Jelesarov (2008).
A survey of the year 2006 literature on applications of isothermal titration calorimetry.
  J Mol Recognit, 21, 1.  
17822439 M.V.de A S Navarro, S.M.Gomes Dias, L.V.Mello, M.T.da Silva Giotto, S.Gavalda, C.Blonski, R.C.Garratt, and D.J.Rigden (2007).
Structural flexibility in Trypanosoma brucei enolase revealed by X-ray crystallography and molecular dynamics.
  FEBS J, 274, 5077-5089.
PDB codes: 2ptw 2ptx 2pty 2ptz 2pu0 2pu1
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