3OIX

Crystal structure of the putative dihydroorotate dehydrogenase from Streptococcus mutans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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This is version 1.2 of the entry. See complete history


Literature

Structure of the putative dihydroorotate dehydrogenase from Streptococcus mutans

Liu, Y.Gao, Z.-Q.Liu, C.-P.Xu, J.-H.Li, L.-F.Ji, C.-N.Su, X.-D.Dong, Y.-H.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 182-187

  • DOI: 10.1107/S1744309110048414
  • Primary Citation of Related Structures:  
    3OIX

  • PubMed Abstract: 
  • Streptococcus mutans is one of the pathogenic species involved in dental caries, especially in the initiation and development stages. Here, the crystal structure of SMU.595, a putative dihydroorotate dehydrogenase (DHOD) from S. mutans, is reported at 2.4 Å resolution ...

    Streptococcus mutans is one of the pathogenic species involved in dental caries, especially in the initiation and development stages. Here, the crystal structure of SMU.595, a putative dihydroorotate dehydrogenase (DHOD) from S. mutans, is reported at 2.4 Å resolution. DHOD is a flavin mononucleotide-containing enzyme which catalyzes the oxidation of L-dihydroorotate to orotate, which is the fourth step and the only redox reaction in the de novo biosynthesis of pyrimidine nucleotides. The reductive lysine-methylation procedure was applied in order to improve the diffraction qualities of the crystals. Analysis of the S. mutans DHOD crystal structure shows that this enzyme is a class 1A DHOD and also suggests potential sites that could be exploited for the design of highly specific inhibitors using the structure-based chemotherapeutic design technique.


    Organizational Affiliation

    Department of Genetics, School of Life Science, Fudan University, Shanghai, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative dihydroorotate dehydrogenase; dihydroorotate oxidaseA, B, C, D345Streptococcus mutansMutation(s): 0 
Gene Names: smu.595
EC: 1.3.3.1 (PDB Primary Data), 1.3.5.2 (PDB Primary Data), 1.3 (UniProt)
UniProt
Find proteins for Q8DVA1 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159))
Explore Q8DVA1 
Go to UniProtKB:  Q8DVA1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DVA1
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
A, B, C, D L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.126α = 90
b = 158.276β = 90
c = 193.351γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description