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Selenomethionine Substitution of Orotidine-5'-monophosphate Decarboxylase from E. coli Causes a Change in Crystal Contacts and Space Group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.344 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Selenomethionine substitution of orotidine-5'-monophosphate decarboxylase causes a change in crystal contacts and space group.

Poulsen, J.C.Harris, P.Jensen, K.F.Larsen, S.

(2001) Acta Crystallogr.,Sect.D 57: 1251-1259


  • PubMed Abstract: 
  • Orotidine 5'-monophosphate decarboxylase (ODCase) catalyses the decarboxylation of orotidine 5'-monophosphate to uridine 5'-monophosphate, the last step in the de novo biosynthesis of uridine 5'-monophosphate. In order to determine the structure of O ...

    Orotidine 5'-monophosphate decarboxylase (ODCase) catalyses the decarboxylation of orotidine 5'-monophosphate to uridine 5'-monophosphate, the last step in the de novo biosynthesis of uridine 5'-monophosphate. In order to determine the structure of ODCase from Escherichia coli by the multi-wavelength anomalous dispersion technique, both native and SeMet-substituted proteins have been produced and purified. During the production of SeMet ODCase, it was observed that SeMet was the only amino acid that it was necessary to add to the defined medium during expression. SeMet-substituted ODCase in complex with the inhibitor 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid crystallizes under similar conditions as the native enzyme. In contrast to the native enzyme, where the crystals belong to the orthorhombic space group P2(1)2(1)2(1), the SeMet-substituted enzyme crystallizes in the monoclinic space group P2(1), with a quadrupling of the volume of the asymmetric unit. Despite the drastic difference in symmetry, the overall crystal packing is effectively identical in the two crystal forms. The change in space group appears to originate in differences in the crystal contacts near the SeMet and Met residues. These differences can be rationalized in terms of SeMet's larger size and hydrophobicity.


    Related Citations: 
    • Structural Basis for the Catalytic Mechanism of a Proficient Enzyme: Orotidine 5'-monophosphate Decarboxylase
      Harris, P.,Poulsen, J.-C.N.,Jensen, K.F.,Larsen, S.
      (2000) Biochemistry 39: 4217


    Organizational Affiliation

    Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
245Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: pyrF
EC: 4.1.1.23
Find proteins for P08244 (Escherichia coli (strain K12))
Go to UniProtKB:  P08244
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMP
Query on BMP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
6-HYDROXYURIDINE-5'-PHOSPHATE
C9 H13 N2 O10 P
UDOBICLZEKUKCV-YXZULKJRSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BMPKi: 0.0088 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.344 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 115.500α = 90.00
b = 149.000β = 115.30
c = 115.600γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
MAR345data collection
CNSrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description