6ENL

INHIBITION OF ENOLASE: THE CRYSTAL STRUCTURES OF ENOLASE-CA2+-PHOSPHOGLYCERATE AND ENOLASE-ZN2+-PHOSPHOGLYCOLATE COMPLEXES AT 2.2-ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Inhibition of enolase: the crystal structures of enolase-Ca2(+)- 2-phosphoglycerate and enolase-Zn2(+)-phosphoglycolate complexes at 2.2-A resolution.

Lebioda, L.Stec, B.Brewer, J.M.Tykarska, E.

(1991) Biochemistry 30: 2823-2827

  • DOI: 10.1021/bi00225a013
  • Primary Citation of Related Structures:  
    6ENL, 5ENL

  • PubMed Abstract: 
  • Enolase is a metalloenzyme which catalyzes the elimination of H2O from 2-phosphoglyceric acid (PGA) to form phosphoenolpyruvate (PEP). Mg2+ and Zn2+ are cofactors which strongly bind and activate the enzyme. Ca2+ also binds strongly but does not produce activity ...

    Enolase is a metalloenzyme which catalyzes the elimination of H2O from 2-phosphoglyceric acid (PGA) to form phosphoenolpyruvate (PEP). Mg2+ and Zn2+ are cofactors which strongly bind and activate the enzyme. Ca2+ also binds strongly but does not produce activity. Phosphoglycolate (PG) is a competitive inhibitor of enolase. The structures of two inhibitory ternary complexes: yeast enolase-Ca2(+)-PGA and yeast enolase-Zn2(+)-PG, were determined by X-ray diffraction to 2.2-A resolution and were refined by crystallographic least-squares to R = 14.8% and 15.7%, respectively, with good geometries of the models. These structures are compared with the structure of the precatalytic ternary complex enolase-Mg2(+)-PGA/PEP (Lebioda & Stec, 1991). In the complex enolase-Ca2(+)-PGA, the PGA molecule coordinates to the Ca2+ ion with the hydroxyl group, as in the precatalytic complex. The conformation of the PGA molecule is however different. In the active complex, the organic part of the PGA molecule is planar, similar to the product. In the inhibitory complex, the carboxylic group is in an orthonormal conformation. In the inhibitory complex enolase-Zn2(+)-PG, the PG molecule coordinates with the carboxylic group in a monodentate mode. In both inhibitory complexes, the conformational changes in flexible loops, which were observed in the precatalytic complex, do not take place. The lack of catalytic metal ion binding suggests that these conformational changes are necessary for the formation of the catalytic metal ion binding site.


    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
    • 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, University of South Carolina, Columbia 29208.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENOLASEA436Saccharomyces cerevisiaeMutation(s): 0 
EC: 4.2.1.11
Find proteins for P00924 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00924 
Go to UniProtKB:  P00924
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGA
Query on PGA

Download Ideal Coordinates CCD File 
B [auth A]2-PHOSPHOGLYCOLIC ACID
C2 H5 O6 P
ASCFNMCAHFUBCO-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Observed: 0.157 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.1α = 90
b = 124.1β = 90
c = 66.9γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1990-11-13 
  • Released Date: 1992-04-15 
  • Deposition Author(s): Lebioda, L., Stec, B.

Revision History  (Full details and data files)

  • Version 1.0: 1992-04-15
    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