1EP2

CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B COMPLEXED WITH OROTATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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 8: 1227-1238

  • DOI: https://doi.org/10.1016/s0969-2126(00)00530-x
  • Primary Citation of Related Structures:  
    1EP1, 1EP2, 1EP3

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)311Lactococcus lactisMutation(s): 0 
EC: 1.3.3.1
UniProt
Find proteins for P54322 (Lactococcus lactis subsp. cremoris (strain MG1363))
Explore P54322 
Go to UniProtKB:  P54322
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54322
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)261Lactococcus lactisMutation(s): 0 
EC: 1.3.3.1
UniProt
Find proteins for P56968 (Lactococcus lactis subsp. cremoris (strain MG1363))
Explore P56968 
Go to UniProtKB:  P56968
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56968
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.190 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 202.42α = 90
b = 202.42β = 90
c = 80.88γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations