1F76

ESCHERICHIA COLI DIHYDROOROTATE DEHYDROGENASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

E. coli Dihydroorotate Dehydrogenase Reveals Structural and Functional Distinction between different classes of dihydroorotate dehydrogenases

Norager, S.Jensen, K.F.Bjornberg, O.Larsen, S.

(2002) Structure 10: 1211-1223


  • PubMed Abstract: 
  • The flavoenzymes dihydroorotate dehydrogenases (DHODs) catalyze the fourth and only redox step in the de novo biosynthesis of UMP. Enzymes belonging to class 2, according to their amino acid sequence, are characterized by having a serine residue as t ...

    The flavoenzymes dihydroorotate dehydrogenases (DHODs) catalyze the fourth and only redox step in the de novo biosynthesis of UMP. Enzymes belonging to class 2, according to their amino acid sequence, are characterized by having a serine residue as the catalytic base and a longer N terminus. The structure of class 2 E. coli DHOD, determined by MAD phasing, showed that the N-terminal extension forms a separate domain. The catalytic serine residue has an environment differing from the equivalent cysteine in class 1 DHODs. Significant differences between the two classes of DHODs were identified by comparison of the E. coli DHOD with the other known DHOD structures, and differences with the class 2 human DHOD explain the variation in their inhibitors.


    Related Citations: 
    • Reduction Reactions of Two Dihydroorotate Dehydrogenases.
      Palfey, B.,Bjornberg, O.,Jensen, K.F.
      (1999) Flavins and Flavoproteins,Proc.13th Int.Symp. --: 615
    • The Activity of Escherichia coli Dihydroorotate Dehydrogenase is Dependent on a Conserved Loop Identified by Sequence Homology, Mutagenesis and Limited Proteolysis.
      Bjornberg, O.,Gruner, A.-C.,Roepstorff, P.,Jensen, K.F.
      (1999) Biochemistry 38: 2899
    • Crystallization and Preliminary X-ray Studies of Membrane-associated Escherichia coli Dihydroorotate Dehydrogenase.
      Rowland, P.,Norager, S.,Jensen, K.F.,Larsen, S.
      (2000) Acta Crystallogr.,Sect.D 56: 659
    • The Dihydroorotate Dehydrogenases of Escherichia coli and Lactococcus Lactis Represent Two Distinct Families of the Enzyme.
      Bjornberg, O.,Jensen, K.F.,Gruner, A.-C.,Ottosen, M.,Sorensen, P.,Rowland, P.,Norager, S.,Larsen, S.
      (1999) Flavins and Flavoproteins,Proc.13th Int.Symp. --: 607


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydroorotate dehydrogenase (quinone)
A, B, D, E
336Escherichia coli (strain K12)Gene Names: pyrD
EC: 1.3.5.2
Find proteins for P0A7E1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7E1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, B, D, E
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
FMT
Query on FMT

Download SDF File 
Download CCD File 
B, D, E
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
ORO
Query on ORO

Download SDF File 
Download CCD File 
A, D
OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, D, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.177 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 119.700α = 90.00
b = 119.700β = 90.00
c = 295.970γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-16
    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: 2014-03-12
    Type: Source and taxonomy, Version format compliance