2XH7

Engineering the enolase active site pocket: Crystal structure of the D321A mutant of yeast enolase 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Engineering the Enolase Magnesium II Binding Site -Implications for its Evolution.

Schreier, B.Hoecker, B.

(2010) Biochemistry 49: 7582

  • DOI: 10.1021/bi100954f
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The glycolytic enzyme enolase catalyzes the reversible elimination of water from 2-phosphoglycerate (2-PGA) to form phosphoenolpyruvate (PEP). Two magnesium ions in the active site are thought to facilitate the reaction by activation of the C2 proton ...

    The glycolytic enzyme enolase catalyzes the reversible elimination of water from 2-phosphoglycerate (2-PGA) to form phosphoenolpyruvate (PEP). Two magnesium ions in the active site are thought to facilitate the reaction by activation of the C2 proton of 2-PGA and charge stabilization of the intermediate. The initial abstraction of a proton from a carboxylic acid is common to all members of the enolase superfamily, yet in all other known members of this superfamily, only one magnesium ion (MgI) per active site is sufficient to promote catalysis. We wanted to further investigate the importance of the second magnesium ion (MgII) for the catalytic mechanism of yeast enolase 1. Toward this end, we removed all MgII coordinating residues and replaced substrate-MgII interactions by introducing positively charged side chains. High-resolution crystal structures and activity assays show that the introduced positively charged side chains effectively prohibit MgII binding but fail to promote catalysis. We conclude that enolase is inactive without MgII, yet control mutants without additional positively charged side chains retain basal enolase activity through binding of magnesium to 2-PGA in an open active site without the help of MgII coordinating residues. Thus, we believe that ancestral enolase activity might have evolved in a member of the enolase superfamily that provides only the necessary catalytic residues and the binding site for MgI. Additionally, precatalytic binding of 2-PGA to the apo state of enolase was observed.


    Organizational Affiliation

    Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENOLASE 1
A, B
443Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
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
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
2PG
Query on 2PG

Download SDF File 
Download CCD File 
A, B
2-PHOSPHOGLYCERIC ACID
C3 H7 O7 P
GXIURPTVHJPJLF-UWTATZPHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.175 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 61.973α = 67.89
b = 62.000β = 78.33
c = 64.320γ = 80.60
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance