1DVJ

CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEXED WITH 6-AZAUMP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

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This is version 1.4 of the entry. See complete history. 


Literature

Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase.

Wu, N., Mo, Y., Gao, J., Pai, E.F.

(2000) Proc Natl Acad Sci U S A 97: 2017-2022

  • DOI: 10.1073/pnas.050417797
  • Primary Citation of Related Structures:  
    1DV7, 1DVJ

  • PubMed Abstract: 

    • Orotidine 5'-monophosphate decarboxylase catalyzes the conversion of orotidine 5'-monophosphate to uridine 5'-monophosphate, the last step in biosynthesis of pyrimidine nucleotides. As part of a Structural Genomics Initiative, the crystal structures of the ligand-free and the6-azauridine 5'-monophosphate-complexed forms have been determined at 1 ...

    Orotidine 5'-monophosphate decarboxylase catalyzes the conversion of orotidine 5'-monophosphate to uridine 5'-monophosphate, the last step in biosynthesis of pyrimidine nucleotides. As part of a Structural Genomics Initiative, the crystal structures of the ligand-free and the6-azauridine 5'-monophosphate-complexed forms have been determined at 1.8 and 1.5 A, respectively. The protein assumes a TIM-barrel fold with one side of the barrel closed off and the other side binding the inhibitor. A unique array of alternating charges (Lys-Asp-Lys-Asp) in the active site prompted us to apply quantum mechanical and molecular dynamics calculations to analyze the relative contributions of ground state destabilization and transition state stabilization to catalysis. The remarkable catalytic power of orotidine 5'-monophosphate decarboxylase is almost exclusively achieved via destabilization of the reactive part of the substrate, which is compensated for by strong binding of the phosphate and ribose groups. The computational results are consistent with a catalytic mechanism that is characterized by Jencks's Circe effect.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
OROTIDINE 5'-PHOSPHATE DECARBOXYLASEA, B, C, D246Methanothermobacter thermautotrophicusMutation(s): 1 
EC: 4.1.1.23
UniProt
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UP6
Query on UP6
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]		6-AZA URIDINE 5'-MONOPHOSPHATE
C8 H12 N3 O9 P
LRVZOSYMNMNQFR-SHUUEZRQSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
UP6 Binding MOAD:  1DVJ Ki: 5.10e+5 (nM) from 1 assay(s)
BindingDB:  1DVJ Ki: 1.24e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.95α = 90
b = 98.62β = 104.03
c = 73.25γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-04-05
    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: 2018-06-06
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2021-11-03
    Changes: Database references, Derived calculations