1GYY

The Crystal Structure of YdcE, a 4-Oxalocrotonate Tautomerase Homologue from Escherichia coli, Confirms the Structural Basis for Oligomer Diversity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The Crystal Structure of Ydce, a 4-Oxalocrotonate Tautomerase Homologue from Escherichia Coli, Confirms the Structural Basis for Oligomer Diversity

Almrud, J.Kern, A.Wang, S.Czerwinski, R.Johnson, W.Murzin, A.Hackert, M.Whitman, C.

(2002) Biochemistry 41: 12010

  • DOI: 10.1021/bi020271h
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The tautomerase superfamily consists of three major families represented by 4-oxalocrotonate tautomerase (4-OT), 5-(carboxymethyl)-2-hydroxymuconate isomerase (CHMI), and macrophage migration inhibitory factor (MIF). The members of this superfamily a ...

    The tautomerase superfamily consists of three major families represented by 4-oxalocrotonate tautomerase (4-OT), 5-(carboxymethyl)-2-hydroxymuconate isomerase (CHMI), and macrophage migration inhibitory factor (MIF). The members of this superfamily are structurally homologous proteins constructed from a simple beta-alpha-beta fold that share a key mechanistic feature; they use an amino-terminal proline, which has an unusually low pK(a), as the general base in a keto-enol tautomerization. Several new members of the 4-OT family have now been identified using PSI-BLAST and categorized into five subfamilies on the basis of multiple-sequence alignments and the conservation of key catalytic and structural residues. The members of subfamily 5, which includes a hypothetical protein designated YdcE from Escherichia coli, are predicted not to form hexamers. The crystal structure of YdcE has been determined to 1.35 A resolution and confirms that it is a dimer. In addition, YdcE complexed with (E)-2-fluoro-p-hydroxycinnamate, identified as a potent competitive inhibitor of this enzyme, as well as N-(2-hydroxyethyl)piperazine-N'-2-ethanesulfonic acid (HEPES) and benzoate are also presented. These latter crystal structures reveal the location of the active site and suggest a mechanism for the observed YdcE-catalyzed tautomerization reaction. The dimeric arrangement of YdcE represents a new structure in the 4-OT family and demonstrates structural diversity within the 4-OT family not previously reported.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Division of Medicinal Chemistry, College of Pharmacy, The University of Texas, Austin, TX 78712-1071, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYPOTHETICAL PROTEIN YDCE
A, B
76Escherichia coliMutation(s): 0 
EC: 5.3.2.1 (PDB Primary Data), 5.3.2 (UniProt)
Find proteins for P31992 (Escherichia coli (strain K12))
Go to UniProtKB:  P31992
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FHC
Query on FHC

Download CCD File 
A, B
2-FLUORO-3-(4-HYDROXYPHENYL)-2E-PROPENEOATE
C9 H6 F O3
SBIZDOWXYPNTOJ-VMPITWQZSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FHCKi:  230000   nM  Binding MOAD
FHCKi :  230000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.7α = 90
b = 46.7β = 90
c = 76.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-02-27
    Changes: Data collection, Experimental preparation, Other