1JRC

The N67A mutant of Lactococcus lactis dihydroorotate dehydrogenase A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Lactococcus lactis dihydroorotate dehydrogenase A mutants reveal important facets of the enzymatic function

Norager, S.Arent, S.Bjornberg, O.Ottosen, M.Lo Leggio, L.Jensen, K.F.Larsen, S.

(2003) J.Biol.Chem. 278: 28812-28822

  • DOI: 10.1074/jbc.M303767200
  • Primary Citation of Related Structures:  1JQV, 1JQX, 1JRB, 1JUB, 1JUE, 1OVD

  • PubMed Abstract: 
  • Dihydroorotate dehydrogenases (DHODs) are flavoenzymes catalyzing the oxidation of (S)-dihydroorotate to orotate in the biosynthesis of UMP, the precursor of all other pyrimidine nucleotides. On the basis of sequence, DHODs can be divided into two cl ...

    Dihydroorotate dehydrogenases (DHODs) are flavoenzymes catalyzing the oxidation of (S)-dihydroorotate to orotate in the biosynthesis of UMP, the precursor of all other pyrimidine nucleotides. On the basis of sequence, DHODs can be divided into two classes, class 1, further divided in subclasses 1A and 1B, and class 2. This division corresponds to differences in cellular location and the nature of the electron acceptor. Herein we report a study of Lactococcus lactis DHODA, a representative of the class 1A enzymes. Based on the DHODA structure we selected seven residues that are highly conserved between both main classes of DHODs as well as three residues representing surface charges close to the active site for site-directed mutagenesis. The availability of both kinetic and structural data on the mutant enzymes allowed us to define the roles individual structural segments play in catalysis. We have also structurally proven the presence of an open active site loop in DHODA and obtained information about the interactions that control movements of loops around the active site. Furthermore, in one mutant structure we observed differences between the two monomers of the dimer, confirming an apparent asymmetry between the two substrate binding sites that was indicated by the kinetic results.


    Related Citations: 
    • Purification and characterisation of dihydroorotate dehydrogenase A from Lactococcus lactis, crystallisation and preliminary X-ray diffraction studies of the enzyme
      Nielsen, F.S.,Rowland, P.,Larsen, S.,Jensen, K.F.
      (1996) Protein Sci. 5: 852
    • The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function
      Rowland, P.,Bjornberg, O.,Nielsen, F.S.,Jensen, K.F.,Larsen, S.
      (1998) Protein Sci. 7: 1269
    • The crystal structure of the flavin containing enzyme dihydroorotate dehydrogenase A from Lactococcus lactis
      Rowland, P.,Nielsen, F.S.,Jensen, K.F.,Larsen, S.
      (1997) Structure 5: 239
    • Active site of dihydroorotate dehydrogenase A from Lactococcus lactis investigated by chemical modification and mutagenesis
      Bjornberg, O.,Rowland, P.,Larsen, S.,Jensen, K.F.
      (1997) Biochemistry 36: 16197


    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 A
A, B
311Lactococcus lactis subsp. cremoris (strain MG1363)Gene Names: pyrDA
EC: 1.3.98.1
Find proteins for A2RJT9 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RJT9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

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

Download SDF File 
Download CCD File 
A, B
OROTIC ACID
C5 H4 N2 O4
PXQPEWDEAKTCGB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
OROKd: 44000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.800α = 90.00
b = 108.090β = 103.89
c = 65.800γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance