1NEL

FLUORIDE INHIBITION OF YEAST ENOLASE: CRYSTAL STRUCTURE OF THE ENOLASE-MG2+-F--PI COMPLEX AT 2.6-ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Fluoride inhibition of yeast enolase: crystal structure of the enolase-Mg(2+)-F(-)-Pi complex at 2.6 A resolution.

Lebioda, L.Zhang, E.Lewinski, K.Brewer, J.M.

(1993) Proteins 16: 219-225

  • DOI: 10.1002/prot.340160302
  • Primary Citation of Related Structures:  
    1NEL

  • PubMed Abstract: 
  • Enolase in the presence of its physiological cofactor Mg2+ is inhibited by fluoride and phosphate ions in a strongly cooperative manner (Nowak, T, Maurer, P. Biochemistry 20:6901, 1981). The structure of the quaternary complex yeast enolase-Mg(2+)-F(-)-Pi has been determined by X-ray diffraction and refined to an R = 16 ...

    Enolase in the presence of its physiological cofactor Mg2+ is inhibited by fluoride and phosphate ions in a strongly cooperative manner (Nowak, T, Maurer, P. Biochemistry 20:6901, 1981). The structure of the quaternary complex yeast enolase-Mg(2+)-F(-)-Pi has been determined by X-ray diffraction and refined to an R = 16.9% for those data with F/sigma (F) > or = 3 to 2.6 A resolution with a good geometry of the model. The movable loops of Pro-35-Ala-45, Val-153-Phe-169, and Asp-255-Asn-266 are in the closed conformation found previously in the precatalytic substrate-enzyme complex. Calculations of molecular electrostatic potential show that this conformation stabilizes binding of negatively charged ligands at the Mg2+ ion more strongly than the open conformation observed in the native enolase. This closed conformation is complementary to the transition state, which also has a negatively charged ion, hydroxide, at Mg2+. The synergism of inhibition by F- and Pi most probably is due to the requirement of Pi for the closed conformation. It is possible that other Mg(2+)-dependent enzymes that have OH- ions bound to the metal ion in the transition state also will be inhibited by fluoride ions.


    Related Citations: 
    • Mechanism of Enolase: The Crystal Structure of Enolase-Mg2+-Phosphoglycerate(Slash) Phosphoenolpyruvate Complex at 2.2-Angstroms Resolution
      Lebioda, L., Stec, B.
      (1991) Biochemistry 30: 2817
    • Inhibition of Enolase: The Crystal Structures of Enolase-Ca2+-Phosphoglycerate and Enolase-Zn2+-Phosphoglycolate Complexes at 2.2-Angstroms Resolution
      Lebioda, L., Stec, B., Brewer, J.M., Tykarska, E.
      (1991) Biochemistry 30: 2823
    • Refined Structure of Yeast Apo-Enolase at 2.25 Angstroms Resolution
      Stec, B., Lebioda, L.
      (1990) J Mol Biol 211: 235
    • Crystal Structure of Holoenzyme Refined at 1.9 Angstroms Resolution: Trigonal-Bipyramidal Geometry of the Cation Binding Site
      Lebioda, L., Stec, B.
      (1989) J Am Chem Soc 111: 8511
    • The Structure of Yeast Enolase at 2.25-Angstroms Resolution. An 8-Fold Beta+Alpha-Barrel with a Novel Beta Beta Alpha Alpha (Beta Alpha)6 Topology
      Lebioda, L., Stec, B., Brewer, J.M.
      (1989) J Biol Chem 264: 3685
    • Crystal Structure of Enolase Indicates that Enolase and Pyruvate Kinase Evolved from a Common Ancestor
      Lebioda, L., Stec, B.
      (1988) Nature 333: 683
    • Crystallization and Preliminary Crystallographic Data for a Tetragonal Form of Yeast Enolase
      Lebioda, L., Brewer, J.M.
      (1984) J Mol Biol 180: 213

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENOLASEA436Saccharomyces cerevisiaeMutation(s): 0 
EC: 4.2.1.11
UniProt
Find proteins for P00924 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00924 
Go to UniProtKB:  P00924
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00924
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
F
Query on F

Download Ideal Coordinates CCD File 
D [auth A]FLUORIDE ION
F
KRHYYFGTRYWZRS-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Observed: 0.169 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.5α = 90
b = 122.5β = 90
c = 67γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other