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: 2.4 Å

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


  • 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 "conformati ...

    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: 
    • Crystal Structure of Enolase Indicates that Enolase and Pyruvate Kinase Evolved from a Common Ancestor
      Lebioda, L.,Stec, B.
      (1988) Nature 333: 683
    • 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
    • Crystallization and Preliminary Crystallographic Data for a Tetragonal Form of Yeast Enolase
      Lebioda, L.,Brewer, J.M.
      (1984) J.Mol.Biol. 180: 213
    • 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
    • Refined Structure of Yeast Apo-Enolase at 2.25 Angstroms Resolution
      Stec, B.,Lebioda, L.
      (1990) J.Mol.Biol. 211: 235
    • 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
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENOLASE
A
436Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: ENO1 (ENOA, HSP48)
EC: 4.2.1.11
Find proteins for P00924 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: ENO1
Go to UniProtKB:  P00924
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
PAH
Query on PAH

Download SDF File 
Download CCD File 
A
PHOSPHONOACETOHYDROXAMIC ACID
C2 H6 N O5 P
LDKRAXXVBWHMRH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PAHKi: 0.015 nM BINDINGMOAD
PAHKi: 0.015 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 124.100α = 90.00
b = 124.100β = 90.00
c = 66.900γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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