3DC8

Crystal structure of dihydropyrimidinase from Sinorhizobium meliloti


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of dihydropyrimidinase from Sinorhizobium meliloti CECT4114: new features in an amidohydrolase family member

Martinez-Rodriguez, S.Martinez-Gomez, A.I.Clemente-Jimenez, J.M.Rodriguez-Vico, F.Garcia-Ruiz, J.M.Las Heras-Vazquez, F.J.Gavira, J.A.

(2010) J.Struct.Biol. 169: 200-208

  • DOI: 10.1016/j.jsb.2009.10.013

  • PubMed Abstract: 
  • The recombinant dihydropyrimidinase from Sinorhizobium meliloti CECT4114 (SmelDhp) has been characterised and its crystal structure elucidated at 1.85A. The global architecture of the protein is reminiscent of that of the amidohydrolase superfamily, ...

    The recombinant dihydropyrimidinase from Sinorhizobium meliloti CECT4114 (SmelDhp) has been characterised and its crystal structure elucidated at 1.85A. The global architecture of the protein is reminiscent of that of the amidohydrolase superfamily, consisting of two domains; an (alpha/beta)(8) TIM-like barrel domain, where the catalytic centre is located, and a smaller beta-sheet sandwich domain of unknown function. The c-terminal tails of each subunit extend toward another monomer in a swapping-like manner, creating a hydrogen bond network which suggests its implication in protein oligomerisation. Mutational and structural evidence suggest the involvement of a conserved tyrosine in the reaction mechanism of the enzyme. SmelDhp presents both hydantoinase and dihydropyrimidinase activities, with higher affinity for the natural six-membered ring substrates. For the five-membered ring substrates, affinity was greater for those with aliphatic and apolar groups in the 5th carbon atom, with the highest rates of hydrolysis for d-5-methyl and d-5-ethyl hydantoin (k(cat)/K(m)=2736+/-380 and 944+/-52M(-1)s(-1), respectively). The optimal conditions for the enzyme activity were found to be 60 degrees C of temperature at pH 8.0. SmelDhp retains 95% of its activity after 6-hour preincubation at 60 degrees C. This is the first dihydropyrimidinase used for the hydrolytic opening of non-natural 6-monosubstituted dihydrouracils, which may be exploited for the production of beta-amino acids.


    Related Citations: 
    • Crystallization and preliminary crystallographic studies of the recombinant dihydropyrimidinase from Sinorhizobium meliloti CECT4114
      Martinez-Rodriguez, S.,Gonzalez-Ramirez, L.A.,Clemente-Jimenez, J.M.,Rodriguez-Vico, F.,Las Heras-Vazquez, F.J.,Gavira, J.A.,Garcia-Ruiz, J.M.
      (2006) Acta Crystallogr.,Sect.F 62: 1223


    Organizational Affiliation

    Dpto. Química Física, Bioquímica y Química Inorgánica, Universidad de Almería, Almería, Spain. srodrig@ual.es




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydropyrimidinase
A, B
490Rhizobium melilotiMutation(s): 0 
Gene Names: dhp (hydA)
EC: 3.5.2.2
Find proteins for Q0PQZ5 (Rhizobium meliloti)
Go to UniProtKB:  Q0PQZ5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
KCX
Query on KCX
A, B
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.148 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 124.887α = 90.00
b = 126.281β = 90.00
c = 196.104γ = 90.00
Software Package:
Software NamePurpose
SAINTdata scaling
REFMACrefinement
SAINTdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2011-08-10
    Type: Database references