Fluoride Inhibition of Enolase: Crystal Structure of the Inhibitory Complex

Experimental Data Snapshot

  • Resolution: 1.36 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.110 
  • R-Value Observed: 0.112 

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Fluoride inhibition of enolase: crystal structure and thermodynamics

Qin, J.Chai, G.Brewer, J.M.Lovelace, L.L.Lebioda, L.

(2006) Biochemistry 45: 793-800

  • DOI: https://doi.org/10.1021/bi051558s
  • Primary Citation of Related Structures:  
    2AKM, 2AKZ

  • PubMed 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.

  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma enolase
A, B
439Homo sapiensMutation(s): 0 
Gene Names: ENO2
UniProt & NIH Common Fund Data Resources
Find proteins for P09104 (Homo sapiens)
Explore P09104 
Go to UniProtKB:  P09104
PHAROS:  P09104
GTEx:  ENSG00000111674 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09104
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TRS

Download Ideal Coordinates CCD File 
C4 H12 N O3
Query on PO4

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E [auth A],
K [auth B]
O4 P
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
I [auth B],
J [auth B]
Query on F

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
L [auth B],
M [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.36 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.110 
  • R-Value Observed: 0.112 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.007α = 90
b = 118.515β = 90
c = 67.189γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SHELXmodel building
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-03-10
    Changes: Advisory, Database references, Derived calculations
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references