1EP3

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.195 

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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 8: 1227-1238

  • DOI: 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 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 D Biol Crystallogr 53: 802
    • 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
    • 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
    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
MoleculeChainsSequence LengthOrganismDetailsImage
DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)A311Lactococcus lactisMutation(s): 0 
EC: 1.3.3.1 (PDB Primary Data), 1.3.1.14 (UniProt)
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)B262Lactococcus 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / 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		 Ligand Interaction
FMN
Query on FMN
Download Ideal Coordinates CCD File 
C [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N		 Ligand Interaction
FES
Query on FES
Download Ideal Coordinates CCD File 
E [auth B]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.195 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 199.89α = 90
b = 199.89β = 90
c = 80.27γ = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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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