1EP1

CRYSTAL STRUCTURE OF LACTOCOCCUS LACTIS DIHYDROOROTATE DEHYDROGENASE B

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.202 

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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
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(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
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  • 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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
D [auth B]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
FMN
Query on FMN
Download Ideal Coordinates CCD File 
C [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
FES
Query on FES
Download Ideal Coordinates CCD File 
E [auth B]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.202 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 202.67α = 90
b = 202.67β = 90
c = 81.11γ = 120
Software Package:
Software NamePurpose
MLPHAREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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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