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PDBsum entry 1ep2
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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1ep2

 

 

 

 

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Contents
Protein chains
305 a.a. *
261 a.a. *
Ligands
FMN
ORO
FAD
FES
Waters ×144
* Residue conservation analysis
PDB id:
1ep2
Name: Oxidoreductase
Title: Crystal structure of lactococcus lactis dihydroorotate dehydrogenase b complexed with orotate
Structure: Dihydroorotate dehydrogenase b (pyrd subunit). Chain: a. Engineered: yes. Dihydroorotate dehydrogenase b (pyrk subunit). Chain: b. Engineered: yes
Source: Lactococcus lactis. Organism_taxid: 1358. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Tetramer (from PDB file)
Resolution:
2.40Å     R-factor:   0.190     R-free:   0.241
Authors: P.Rowland,S.Norager,K.F.Jensen,S.Larsen
Key ref:
P.Rowland et al. (2000). Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster. Structure, 8, 1227-1238. PubMed id: 11188687 DOI: 10.1016/S0969-2126(00)00530-X
Date:
27-Mar-00     Release date:   17-Jan-01    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P54322  (PYRDB_LACLM) -  Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit from Lactococcus lactis subsp. cremoris (strain MG1363)
Seq:
Struc: 		311 a.a.
305 a.a.*
Protein chain
Pfam   ArchSchema ?
P56968  (PYRK_LACLM) -  Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit from Lactococcus lactis subsp. cremoris (strain MG1363)
Seq:
Struc: 		262 a.a.
261 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class 2: Chain A: E.C.1.3.1.14  - dihydroorotate dehydrogenase (NAD(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (S)-dihydroorotate + NAD+ = orotate + NADH + H+
(S)-dihydroorotate
Bound ligand (Het Group name = ORO)
corresponds exactly 		+ NAD(+)
 = orotate
 + NADH
 + H(+)
      Cofactor: FAD; FMN; Iron-sulfur
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
FMN
Bound ligand (Het Group name = FMN) corresponds exactly 		Iron-sulfur
   Enzyme class 3: Chain B: E.C.1.3.3.1  - Transferred entry: 1.3.98.1.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: (S)-dihydroorotate + O2 = orotate + H2O2
(S)-dihydroorotate
Bound ligand (Het Group name = ORO)
corresponds exactly 		+ O(2)
 = orotate
 + H(2)O(2)
      Cofactor: FAD; FMN
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
FMN
Bound ligand (Het Group name = FMN) corresponds exactly
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(00)00530-X Structure 8:1227-1238 (2000)
PubMed id: 11188687  
 
 
Structure of dihydroorotate dehydrogenase B: electron transfer between two flavin groups bridged by an iron-sulphur cluster.
P.Rowland, S.Nørager, K.F.Jensen, S.Larsen.
 
  ABSTRACT  
 
BACKGROUND: 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. RESULTS: Crystal structures have been determined for DHODB and its product complex. The DHODB heterotetramer is composed of two closely interacting PyrDB-PyrK dimers with the [2Fe-2S] cluster in their interface centered between the FMN and FAD groups. Conformational changes are observed between the complexed and uncomplexed state of the enzyme for the loop carrying the catalytic cysteine residue and one of the lysines interacting with FMN, which is important for substrate binding. CONCLUSIONS: A dimer of two PyrDB subunits resembling the family 1A enzymes forms the central core of DHODB. PyrK belongs to the NADPH ferredoxin reductase superfamily. The binding site for NAD+ has been deduced from the similarity to these proteins. The orotate binding in DHODB is similar to that in the family 1A enzymes. The close proximity of the three redox centers makes it possible to propose a possible electron transfer pathway involving residues conserved among the family 1B DHODs.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. The Environment of the Two Flavin Groups and the Orotate Binding Site in DHODB(a) The environment of the FMN group in the uncomplexed PyrDB subunit with an open catalytic loop. Water molecules are shown as cyan spheres.(b) The DHODB-orotate complex structure showing the same view of the FMN group as in Figure 6a and containing a closed but slightly disordered catalytic loop.(c) A closeup view of the environment of the bound orotate in the complexed structure.(d) The environment of the FAD group in PyrK subunit in the uncomplexed structure. No significant changes were observed in the structure of the orotate complex

 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 1227-1238) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20334617 M.A.Phillips, and P.K.Rathod (2010).
Plasmodium dihydroorotate dehydrogenase: a promising target for novel anti-malarial chemotherapy.
  Infect Disord Drug Targets, 10, 226-239.  
19530672 R.L.Fagan, and B.A.Palfey (2009).
Roles in binding and chemistry for conserved active site residues in the class 2 dihydroorotate dehydrogenase from Escherichia coli.
  Biochemistry, 48, 7169-7178.  
19694481 R.L.Kow, J.R.Whicher, C.A.McDonald, B.A.Palfey, and R.L.Fagan (2009).
Disruption of the proton relay network in the class 2 dihydroorotate dehydrogenase from Escherichia coli.
  Biochemistry, 48, 9801-9809.  
19060157 S.Kawasaki, T.Satoh, M.Todoroki, and Y.Niimura (2009).
b-type dihydroorotate dehydrogenase is purified as a H2O2-forming NADH oxidase from Bifidobacterium bifidum.
  Appl Environ Microbiol, 75, 629-636.  
18312275 T.L.Arakaki, F.S.Buckner, J.R.Gillespie, N.A.Malmquist, M.A.Phillips, O.Kalyuzhniy, J.R.Luft, G.T.Detitta, C.L.Verlinde, W.C.Van Voorhis, W.G.Hol, and E.A.Merritt (2008).
Characterization of Trypanosoma brucei dihydroorotate dehydrogenase as a possible drug target; structural, kinetic and RNAi studies.
  Mol Microbiol, 68, 37-50.
PDB code: 2b4g
17594507 J.L.Chung, W.Wang, and P.E.Bourne (2007).
High-throughput identification of interacting protein-protein binding sites.
  BMC Bioinformatics, 8, 223.  
17329250 N.A.Malmquist, J.Baldwin, and M.A.Phillips (2007).
Detergent-dependent kinetics of truncated Plasmodium falciparum dihydroorotate dehydrogenase.
  J Biol Chem, 282, 12678-12686.  
16624811 J.P.Combe, J.Basran, P.Hothi, D.Leys, S.E.Rigby, A.W.Munro, and N.S.Scrutton (2006).
Lys-D48 is required for charge stabilization, rapid flavin reduction, and internal electron transfer in the catalytic cycle of dihydroorotate dehydrogenase B of Lactococcus lactis.
  J Biol Chem, 281, 17977-17988.  
15935511 M.Kilstrup, K.Hammer, P.Ruhdal Jensen, and J.Martinussen (2005).
Nucleotide metabolism and its control in lactic acid bacteria.
  FEMS Microbiol Rev, 29, 555-590.  
15044733 M.Hansen, J.Le Nours, E.Johansson, T.Antal, A.Ullrich, M.Löffler, and S.Larsen (2004).
Inhibitor binding in a class 2 dihydroorotate dehydrogenase causes variations in the membrane-associated N-terminal domain.
  Protein Sci, 13, 1031-1042.
PDB codes: 1uum 1uuo
12732650 S.Nørager, S.Arent, O.Björnberg, M.Ottosen, L.Lo Leggio, K.F.Jensen, and S.Larsen (2003).
Lactococcus lactis dihydroorotate dehydrogenase A mutants reveal important facets of the enzymatic function.
  J Biol Chem, 278, 28812-28822.
PDB codes: 1jqv 1jqx 1jrb 1jrc 1jub 1jue 1ovd
11983710 A.C.Bishop, J.Xu, R.C.Johnson, P.Schimmel, and V.de Crécy-Lagard (2002).
Identification of the tRNA-dihydrouridine synthase family.
  J Biol Chem, 277, 25090-25095.  
12381841 M.B.Ottosen, O.Björnberg, S.Nørager, S.Larsen, B.A.Palfey, and K.F.Jensen (2002).
The dimeric dihydroorotate dehydrogenase A from Lactococcus lactis dissociates reversibly into inactive monomers.
  Protein Sci, 11, 2575-2583.  
12220493 S.Nørager, K.F.Jensen, O.Björnberg, and S.Larsen (2002).
E. coli dihydroorotate dehydrogenase reveals structural and functional distinctions between different classes of dihydroorotate dehydrogenases.
  Structure, 10, 1211-1223.
PDB code: 1f76
11284694 B.A.Palfey, O.Björnberg, and K.F.Jensen (2001).
Insight into the chemistry of flavin reduction and oxidation in Escherichia coli dihydroorotate dehydrogenase obtained by rapid reaction studies.
  Biochemistry, 40, 4381-4390.  
11468361 G.Pujadas, and J.Palau (2001).
Molecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site.
  Protein Sci, 10, 1645-1657.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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