Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 69657.15 
• Atom Count: 4868 
• Residue Count: 622 
• Unique protein chains: 1

1JRB

The P56A mutant of Lactococcus lactis dihydroorotate dehydrogenase A

• DOI: 10.2210/pdb1JRB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Lactococcus lactis subsp. cremoris (strain MG1363)
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2001-08-13 Released: 2003-09-09 
• Deposition Author(s): Norager, S., Arent, S., Bjornberg, O., Ottosen, M., Lo Leggio, L., Jensen, K.F., Larsen, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.236 
• R-Value Work: 0.196 

Literature

Lactococcus lactis dihydroorotate dehydrogenase A mutants reveal important facets of the enzymatic function

Norager, S., Arent, S., Bjornberg, O., Ottosen, M., Lo Leggio, L., Jensen, K.F., Larsen, S.

(2003) J.Biol.Chem. 278: 28812-28822

• PubMed: 12732650 
• DOI: 10.1074/jbc.M303767200
• Primary Citation of Related Structures:  
  1OVD, 1JUE, 1JUB, 1JRC, 1JQX, 1JQV


• PubMed Abstract: 
  

Dihydroorotate dehydrogenases (DHODs) are flavoenzymes catalyzing the oxidation of (S)-dihydroorotate to orotate in the biosynthesis of UMP, the precursor of all other pyrimidine nucleotides. On the basis of sequence, DHODs can be divided into two classes, class 1, further divided in subclasses 1A and 1B, and class 2. This division corresponds to differences in cellular location and the nature of the electron acceptor. Herein we report a study of Lactococcus lactis DHODA, a representative of the class 1A enzymes. Based on the DHODA structure we selected seven residues that are highly conserved between both main classes of DHODs as well as three residues representing surface charges close to the active site for site-directed mutagenesis. The availability of both kinetic and structural data on the mutant enzymes allowed us to define the roles individual structural segments play in catalysis. We have also structurally proven the presence of an open active site loop in DHODA and obtained information about the interactions that control movements of loops around the active site. Furthermore, in one mutant structure we observed differences between the two monomers of the dimer, confirming an apparent asymmetry between the two substrate binding sites that was indicated by the kinetic results.

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Related Citations: 

• The crystal structure of Lactococcus lactis dihydroorotate dehydrogenase A complexed with the enzyme reaction product throws light on its enzymatic function
  Rowland, P.,Bjornberg, O.,Nielsen, F.S.,Jensen, K.F.,Larsen, S.
  (1998) Protein Sci. 7: 1269
• Purification and characterisation of dihydroorotate dehydrogenase A from Lactococcus lactis, crystallisation and preliminary X-ray diffraction studies of the enzyme
  Nielsen, F.S.,Rowland, P.,Larsen, S.,Jensen, K.F.
  (1996) Protein Sci. 5: 852
• The crystal structure of the flavin containing enzyme dihydroorotate dehydrogenase A from Lactococcus lactis
  Rowland, P.,Nielsen, F.S.,Jensen, K.F.,Larsen, S.
  (1997) Structure 5: 239
• Active site of dihydroorotate dehydrogenase A from Lactococcus lactis investigated by chemical modification and mutagenesis
  Bjornberg, O.,Rowland, P.,Larsen, S.,Jensen, K.F.
  (1997) Biochemistry 36: 16197




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Organizational Affiliation: 

Centre for Crystallographic Studies, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
dihydroorotate dehydrogenase A	A, B	311	Lactococcus lactis subsp. cremoris (strain MG1363)	Mutation(s): 1  Gene Names: pyrDA EC: 1.3.98.1
Find proteins for A2RJT9 (Lactococcus lactis subsp. cremoris (strain MG1363)) Go to UniProtKB:  A2RJT9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
FMN	A, B	FLAVIN MONONUCLEOTIDE RIBOFLAVIN MONOPHOSPHATE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
ORO	A, B	OROTIC ACID C5 H4 N2 O4 PXQPEWDEAKTCGB-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ORO	Kd: 1450000 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.236 
• R-Value Work: 0.196 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 53.074	α = 90.00
b = 108.822	β = 103.92
c = 66.453	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-08-13 
• Released Date: 2003-09-09 
• Deposition Author(s): Norager, S., Arent, S., Bjornberg, O., Ottosen, M., Lo Leggio, L., Jensen, K.F., Larsen, S.

Revision History 

• Version 1.0: 2003-09-09
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-05-23
  Type: Data collection