Crystal structure of orotidine monophosphate decarboxylase mutant D70A complexed with UMP

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

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Mapping the active site-ligand interactions of orotidine 5'-monophosphate decarboxylase by crystallography.

Wu, N.Gillon, W.Pai, E.F.

(2002) Biochemistry 41: 4002-4011

  • DOI: https://doi.org/10.1021/bi015758p
  • Primary Citation of Related Structures:  
    1KLY, 1KLZ, 1KM0, 1KM1, 1KM2, 1KM3, 1KM4, 1KM5, 1KM6

  • PubMed Abstract: 

    The crystal structures of orotidine 5'-monophosphate decarboxylases from four different sources have been published recently. However, the detailed mechanism of catalysis of the most proficient enzyme known to date remains elusive. As the ligand-protein interactions at the orotate binding site are crucial to the understanding of this enzyme, we mutated several of the residues surrounding the aromatic part of the substrate, individually and in combination. The ensuing effects on enzyme structure and stability were characterized by X-ray crystallography of inhibitor, product, or substrate complexes and by chemical denaturation with guanidine hydrochloride, respectively. The results are consistent with the residues K42D70K72D75B being charged and forming an 'alternate charge network' around the reactive part of the substrate. In addition to exerting charge-charge repulsion on the orotate carboxylate, Asp70 also makes a crucial contribution to enzyme stability. Consequently, orotidine 5'-monophosphate decarboxylases seem to require the presence of a negative charge at this position for catalysis as well as for correct and stable folding.

  • Organizational Affiliation

    Department of Biochemistry, Centres of Excellence, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OROTIDINE 5'-PHOSPHATE DECARBOXYLASE247Methanothermobacter thermautotrophicusMutation(s): 2 
Find proteins for O26232 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Explore O26232 
Go to UniProtKB:  O26232
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO26232
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on U

Download Ideal Coordinates CCD File 
C9 H13 N2 O9 P
Query on CL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
Binding Affinity Annotations 
IDSourceBinding Affinity
U BindingDB:  1KLZ Ki: 3.30e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.225α = 90
b = 103.295β = 90
c = 74.582γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-14
    Changes: Data collection