3GDL

Crystal structure of the orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae complexed with 6-azauridine 5'-monophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.

Chan, K.K.Wood, B.M.Fedorov, A.A.Fedorov, E.V.Imker, H.J.Amyes, T.L.Richard, J.P.Almo, S.C.Gerlt, J.A.

(2009) Biochemistry 48: 5518-5531

  • DOI: https://doi.org/10.1021/bi900623r
  • Primary Citation of Related Structures:  
    3G18, 3G1A, 3G1D, 3G1F, 3G1H, 3G1S, 3G1V, 3G1X, 3G1Y, 3G22, 3G24, 3GDK, 3GDL, 3GDR, 3GDT

  • PubMed Abstract: 

    The reaction catalyzed by orotidine 5'-monophosphate decarboxylase (OMPDC) involves a stabilized anionic intermediate, although the structural basis for the rate acceleration (k(cat)/k(non), 7.1 x 10(16)) and proficiency [(k(cat)/K(M))/k(non), 4.8 x 10(22) M(-1)] is uncertain. That the OMPDCs from Methanothermobacter thermautotrophicus (MtOMPDC) and Saccharomyces cerevisiae (ScOMPDC) catalyze the exchange of H6 of the UMP product with solvent deuterium allows an estimate of a lower limit on the rate acceleration associated with stabilization of the intermediate and its flanking transition states (>or=10(10)). The origin of the "missing" contribution, or=10(10)), is of interest. Based on structures of liganded complexes, unfavorable electrostatic interactions between the substrate carboxylate group and a proximal Asp (Asp 70 in MtOMPDC and Asp 91 in ScOMPDC) have been proposed to contribute to the catalytic efficiency [Wu, N., Mo, Y., Gao, J., and Pai, E. F. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 2017-2022]. We investigated that hypothesis by structural and functional characterization of the D70N and D70G mutants of MtOMPDC and the D91N mutant of ScOMPDC. The substitutions for Asp 70 in MtOMPDC significantly decrease the value of k(cat) for decarboxylation of FOMP (a more reactive substrate analogue) but have little effect on the value of k(ex) for exchange of H6 of FUMP with solvent deuterium; the structures of wild-type MtOMPDC and its mutants are superimposable when complexed with 6-azaUMP. In contrast, the D91N mutant of ScOMPDC does not catalyze exchange of H6 of FUMP; the structures of wild-type ScOMPDC and its D91N mutant are not superimposable when complexed with 6-azaUMP, with differences in both the conformation of the active site loop and the orientation of the ligand vis a vis the active site residues. We propose that the differential effects of substitutions for Asp 70 of MtOMPDC on decarboxylation and exchange provide additional evidence for a carbanionic intermediate as well as the involvement of Asp 70 in substrate destabilization.


  • Organizational Affiliation

    Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orotidine 5'-phosphate decarboxylase
A, B
267Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: URA3YEL021W
EC: 4.1.1.23
UniProt
Find proteins for P03962 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P03962 
Go to UniProtKB:  P03962
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03962
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UP6
Query on UP6

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
6-AZA URIDINE 5'-MONOPHOSPHATE
C8 H12 N3 O9 P
LRVZOSYMNMNQFR-SHUUEZRQSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
UP6 BindingDB:  3GDL Ki: 64 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.73α = 90
b = 80.356β = 125.12
c = 77.566γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
BALBESphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description