1EP3

CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B. DATA COLLECTED UNDER CRYOGENIC CONDITIONS.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster.

Rowland, P.Norager, S.Jensen, K.F.Larsen, S.

(2000) Structure Fold.Des. 8: 1227-1238

  • Primary Citation of Related Structures:  1EP1, 1EP2

  • PubMed Abstract: 
  • The fourth step and only redox reaction in pyrimidine de novo biosynthesis is catalyzed by the flavoprotein dihydroorotate dehydrogenase (DHOD). Based on their sequences, DHODs are grouped into two major families. Lactococcus lactis is one of the few ...

    The fourth step and only redox reaction in pyrimidine de novo biosynthesis is catalyzed by the flavoprotein dihydroorotate dehydrogenase (DHOD). Based on their sequences, DHODs are grouped into two major families. Lactococcus lactis is one of the few organisms with two DHODs, A and B, belonging to each of the two subgroups of family 1. The B enzyme (DHODB) is a prototype for DHODs in Gram-positive bacteria that use NAD+ as the second substrate. DHODB is a heterotetramer composed of two different proteins (PyrDB and PyrK) and three different cofactors: FMN, FAD, and a [2Fe-2S] cluster.


    Related Citations: 
    • Crystallization and Preliminary X-ray Diffraction Analysis of the Heterotetrameric Dihydroorotate Dehydrogenase B of Lactococcus lactis, a Flavoprotein Enzyme System Consisting of two PyrDB Subunits and Two Iron-Sulfur Cluster Containing PyrK Subunits
      Rowland, P.,Nielsen, F.S.,Jensen, K.F.,Larsen, S.
      (1997) Acta Crystallogr.,Sect.D 53: 802
    • Roles of three prosthetic groups in tetrameric Dihydroorotate dehydrogenase B from Lactococcus lactis
      Jensen, K.F.,Bjornberg, O.,Nielsen, F.S.,Ottosen, M.,Sorensen, P.G.,Rowland, P.,Norager, S.,Larsen, S.
      (1999) Flavins and Flavoproteins 13th: 599
    • The B Form of Dihydroorotate Dehydrogenase from Lactococcus lactis Consists of two Different Subunits, Encoded by the pyrDb and PyrK Genes, and Contains FMN, FAD and [FeS] Redox Centers
      Nielsen, F.S.,Andersen, P.S.,Jensen, K.F.
      (1996) J.Biol.Chem. 271: 29359


    Organizational Affiliation

    Centre for Crystallographic Studies, Department of Chemistry, University of Copenhagen, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)
A
311Lactococcus lactis subsp. cremoris (strain MG1363)Gene Names: pyrDB
EC: 1.3.1.14
Find proteins for P54322 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  P54322
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)
B
262Lactococcus lactis subsp. cremoris (strain MG1363)Gene Names: pyrK
Find proteins for P56968 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  P56968
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

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

Download SDF File 
Download CCD File 
B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
B
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.195 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 199.890α = 90.00
b = 199.890β = 90.00
c = 80.270γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-01-17
    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