Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 63.09 kDa 
• Atom Count: 4854 
• Modelled Residue Count: 572 
• Deposited Residue Count: 573 
• Unique protein chains: 2

1EP3

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

• DOI: 10.2210/pdb1EP3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Lactococcus lactis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-03-27 Released: 2001-01-17 
• Deposition Author(s): Rowland, P., Norager, S., Jensen, K.F., Larsen, S.

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Experimental Data Snapshot

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

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

• PubMed: 11188687 
• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROOROTATE DEHYDROGENASE B (PYRD SUBUNIT)	A	311	Lactococcus lactis	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROOROTATE DEHYDROGENASE B (PYRK SUBUNIT)	B	262	Lactococcus lactis	Mutation(s): 0  EC: 1.3.3.1
UniProt
Find proteins for P56968 (Lactococcus lactis subsp. cremoris (strain MG1363)) Explore P56968  Go to UniProtKB:  P56968

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD (Subject of Investigation/LOI)	D [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
FMN (Subject of Investigation/LOI)	C [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
FES	E [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

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 = 199.89	α = 90
b = 199.89	β = 90
c = 80.27	γ = 120

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2000-03-27 
• Released Date: 2001-01-17 
Deposition Author(s): Rowland, P., Norager, S., Jensen, K.F., Larsen, S.

Revision History  

• 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