1JJK

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: 3.00 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.344 
  • R-Value Observed: 0.344 

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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 D Biol Crystallogr 57: 1251-1259

  • DOI: https://doi.org/10.1107/s0907444901010393
  • Primary Citation of Related Structures:  
    1JJK

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
245Escherichia coliMutation(s): 9 
EC: 4.1.1.23
UniProt
Find proteins for P08244 (Escherichia coli (strain K12))
Explore P08244 
Go to UniProtKB:  P08244
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08244
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BMP
Query on BMP

Download Ideal Coordinates CCD File 
AA [auth K]
BA [auth L]
CA [auth M]
DA [auth N]
EA [auth O]
AA [auth K],
BA [auth L],
CA [auth M],
DA [auth N],
EA [auth O],
FA [auth P],
Q [auth A],
R [auth B],
S [auth C],
T [auth D],
U [auth E],
V [auth F],
W [auth G],
X [auth H],
Y [auth I],
Z [auth J]
6-HYDROXYURIDINE-5'-PHOSPHATE
C9 H13 N2 O10 P
UDOBICLZEKUKCV-YXZULKJRSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
BMP PDBBind:  1JJK Ki: 8.80e-3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.344 
  • R-Value Observed: 0.344 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.5α = 90
b = 149β = 115.3
c = 115.6γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
MAR345data collection
CCP4data 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: 2001-08-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description