1P43

REVERSE PROTONATION IS THE KEY TO GENERAL ACID-BASE CATALYSIS IN ENOLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Reverse protonation is the key to general acid-base catalysis in enolase

Sims, P.A.Larsen, T.M.Poyner, R.R.Cleland, W.W.Reed, G.H.

(2003) Biochemistry 42: 8298-8306

  • DOI: 10.1021/bi0346345
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The pH dependence of enolase catalysis was studied to understand how enolase is able to utilize both general acid and general base catalysis in each direction of the reaction at near-neutral pHs. Wild-type enolase from yeast was assayed in the dehydr ...

    The pH dependence of enolase catalysis was studied to understand how enolase is able to utilize both general acid and general base catalysis in each direction of the reaction at near-neutral pHs. Wild-type enolase from yeast was assayed in the dehydration reaction (2-phospho-D-glycerate --> phosphoenolpyruvate + H(2)O) at different pHs. E211Q, a site-specific variant of enolase that catalyzes the exchange of the alpha-proton of 2-phospho-D-glycerate but not the complete dehydration, was assayed in a (1)H/(2)H exchange reaction at different pDs. Additionally, crystal structures of E211Q and E168Q were obtained at 2.0 and 1.8 A resolution, respectively. Analysis of the pH profile of k(cat)/K(Mg) for wild-type enolase yielded macroscopic pK(a) estimates of 7.4 +/- 0.3 and 9.0 +/- 0.3, while the results of the pD profile of the exchange reaction of E211Q led to a pK(a) estimate of 9.5 +/- 0.1. These values permit estimates of the four microscopic pK(a)s that describe the four relevant protonation states of the acid/base catalytic groups in the active site. The analysis indicates that the dehydration reaction is catalyzed by a small fraction of enzyme that is reverse-protonated (i.e., Lys345-NH(2), Glu211-COOH), whereas the hydration reaction is catalyzed by a larger fraction of the enzyme that is typically protonated (i.e., Lys345-NH(3)(+), Glu211-COO(-)). These two forms of the enzyme coexist in a constant, pH-independent ratio. The structures of E211Q and E168Q both show virtually identical folds and active-site architectures (as compared to wild-type enolase) and thus provide additional support to the conclusions reported herein. Other enzymes that require both general acid and general base catalysis likely require reverse protonation of catalytic groups in one direction of the reaction.


    Organizational Affiliation

    Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53726, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Enolase 1
A, B
436Saccharomyces 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: 0.213 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 107.300α = 90.00
b = 115.100β = 90.00
c = 72.400γ = 90.00
Software Package:
Software NamePurpose
LSCALEdata reduction
SAINTdata reduction
SAINTdata scaling
LSCALEdata scaling
CNSrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model
  • Version 1.4: 2017-10-11
    Type: Refinement description