Crystal structure of E112Q mutant of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L-threonohydroxamate 4-phosphate

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Evolution of Enzymatic Activities in the Orotidine 5'-Monophosphate Decarboxylase Suprafamily: Crystallographic Evidence for a Proton Relay System in the Active Site of 3-Keto-l-gulonate 6-Phosphate Decarboxylase(,)

Wise, E.L.Yew, W.S.Gerlt, J.A.Rayment, I.

(2004) Biochemistry 43: 6438-6446

  • DOI: https://doi.org/10.1021/bi0497392
  • Primary Citation of Related Structures:  
    1SO3, 1SO4, 1SO5, 1SO6

  • PubMed Abstract: 

    3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC), a member of the orotidine monophosphate decarboxylase (OMPDC) suprafamily, catalyzes the Mg(2+)-dependent decarboxylation of 3-keto-L-gulonate 6-phosphate to L-xylulose 5-phosphate. Structural and biochemical evidence suggests that the KGPDC reaction proceeds via a Mg(2+)-stabilized 1,2-cis-enediolate intermediate. Protonation of the enediolate intermediate occurs in a nonstereospecific manner to form L-xylulose 5-phosphate. Although the exact mechanism of proton delivery is not known, Glu112, His136, and Arg139 have been implicated in this process [Yew, W. S., Wise, E., Rayment, I., and Gerlt, J. A. (2004) Biochemistry 43, 6427-6437]. Surprisingly, single amino acid substitutions of these positions do not substantially reduce catalytic activity but rather alter the stereochemical course of the reaction. Here, we report the X-ray crystal structures of four mutants, K64A, H136A, E112Q, and E112Q/H136A, each determined in the presence of L-threonohydroxamate 4-phosphate, an analogue of the enediolate intermediate, to 1.7, 1.9, 1.8, and 1.9 A resolution, respectively. These structures reveal that substitutions of Lys64, Glu112, and His136 cause changes in the positions of the intermediate analogue and two active site water molecules that were previously identified as possible proton donors. These changes correlate with the observed alterations in the reaction stereochemistry for these mutants, thereby supporting a reaction mechanism in which water molecules competitively shuttle protons from the side chains of His136 and Arg139 to alternate faces of the cis-enediolate intermediate. These studies further underscore the wide variation in the reaction mechanisms in the OMPDC suprafamily.

  • Organizational Affiliation

    Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3-keto-L-gulonate 6-phosphate decarboxylase
A, B
216Escherichia coliMutation(s): 1 
Gene Names: ulaD
EC: 4.1.2 (PDB Primary Data), (UniProt)
Find proteins for P39304 (Escherichia coli (strain K12))
Explore P39304 
Go to UniProtKB:  P39304
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39304
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.158 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.756α = 90
b = 41.849β = 97.24
c = 91.009γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations