1KM3

crystal structure of ODCase mutant K42A complexed with 6-azaUMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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

  • Primary Citation of Related Structures:  1KLY, 1KLZ, 1KM1, 1KM0, 1KM2, 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-prot ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
A
247Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)Gene Names: pyrF
EC: 4.1.1.23
Find proteins for O26232 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Go to UniProtKB:  O26232
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UP6
Query on UP6

Download SDF File 
Download CCD File 
A
6-AZA URIDINE 5'-MONOPHOSPHATE
6-AZA-UMP
C8 H12 N3 O9 P
LRVZOSYMNMNQFR-SHUUEZRQSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UP6Ki: 12400 nM (98) BINDINGDB
UP6Ki: 12400 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.162 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 58.355α = 90.00
b = 103.178β = 90.00
c = 73.512γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance