1ELS

CATALYTIC METAL ION BINDING IN ENOLASE: THE CRYSTAL STRUCTURE OF ENOLASE-MN2+-PHOSPHONOACETOHYDROXAMATE COMPLEX AT 2.4 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Catalytic metal ion binding in enolase: the crystal structure of an enolase-Mn2+-phosphonoacetohydroxamate complex at 2.4-A resolution.

Zhang, E.Hatada, M.Brewer, J.M.Lebioda, L.

(1994) Biochemistry 33: 6295-6300

  • DOI: https://doi.org/10.1021/bi00186a032
  • Primary Citation of Related Structures:  
    1ELS

  • PubMed Abstract: 
  • Enolase, a glycolytic enzyme that catalyzes the dehydration of 2-phospho-D-glycerate (PGA) to form phosphoenolpyruvate (PEP), requires two divalent metal ions per active site for activity. The first metal ion, traditionally referred to as "conformational", binds in a high-affinity site I ...

    Enolase, a glycolytic enzyme that catalyzes the dehydration of 2-phospho-D-glycerate (PGA) to form phosphoenolpyruvate (PEP), requires two divalent metal ions per active site for activity. The first metal ion, traditionally referred to as "conformational", binds in a high-affinity site I. The second metal ion, "catalytic", binds in site II only in the presence of a substrate or substrate analogue and with much lower affinity for the physiological cofactor Mg2+. While the high-affinity site has been well characterized, the position of the lower affinity site has not been established so far. Here, we report the structure of the quaternary complex between enolase, the transition-state analogue phosphonoacetohydroxamate (PhAH), and two Mn2+ ions. The structure has been refined by using 16 561 reflections with F/sigma (F) > or = 3 to an R = 0.165 with average deviations of bond lengths and bond angles from ideal values of 0.013 A and 3.1 degrees, respectively. The "catalytic" metal ion is coordinated to two oxygen atoms of the phosphono moiety of PhAH and to the carbonyl oxygen of Gly37. Most likely, disordered water molecules complement its coordination sphere. The interaction with the site II metal ion must stabilize negative charge on the phosphate group and produce electron withdrawal from carbon 2 of the substrate, facilitating proton abstraction from carbon 2, the rate-limiting step in the catalytic process. The Gly37 residue is located in the flexible loop Ser36-His43, which assumes an "open" conformation in the absence of substrate and a "closed" conformation in the presence of a substrate.(ABSTRACT TRUNCATED AT 250 WORDS)


    Related Citations: 
    • Fluoride Inhibition of Yeast Enolase: Crystal Structure of the Enolase-Mg2+-F--PI Complex at 2.6-Angstroms Resolution
      Lebioda, L., Zhang, E., Lewinski, K., Brewer, J.M.
      (1993) Proteins 16: 219
    • 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PAH
Query on PAH

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHONOACETOHYDROXAMIC ACID
C2 H6 N O5 P
LDKRAXXVBWHMRH-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
PAH PDBBind:  1ELS Ki: 0.02 (nM) from 1 assay(s)
Binding MOAD:  1ELS Ki: 0.02 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Observed: 0.165 
  • 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

Revision History  (Full details and data files)

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