4XJC

dCTP deaminase-dUTPase from Bacillus halodurans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Bacillus halodurans Strain C125 Encodes and Synthesizes Enzymes from Both Known Pathways To Form dUMP Directly from Cytosine Deoxyribonucleotides.

Oehlenschlger, C.B.Lvgreen, M.N.Reinauer, E.Lehtinen, E.Pind, M.L.Harris, P.Martinussen, J.Willemoes, M.

(2015) Appl.Environ.Microbiol. 81: 3395-3404

  • DOI: 10.1128/AEM.00268-15

  • PubMed Abstract: 
  • Analysis of the genome of Bacillus halodurans strain C125 indicated that two pathways leading from a cytosine deoxyribonucleotide to dUMP, used for dTMP synthesis, were encoded by the genome of the bacterium. The genes that were responsible, the comE ...

    Analysis of the genome of Bacillus halodurans strain C125 indicated that two pathways leading from a cytosine deoxyribonucleotide to dUMP, used for dTMP synthesis, were encoded by the genome of the bacterium. The genes that were responsible, the comEB gene and the dcdB gene, encoding dCMP deaminase and the bifunctional dCTP deaminase:dUTPase (DCD:DUT), respectively, were both shown to be expressed in B. halodurans, and both genes were subject to repression by the nucleosides thymidine and deoxycytidine. The latter nucleoside presumably exerts its repression after deamination by cytidine deaminase. Both comEB and dcdB were cloned, overexpressed in Escherichia coli, and purified to homogeneity. Both enzymes were active and displayed the expected regulatory properties: activation by dCTP for dCMP deaminase and dTTP inhibition for both enzymes. Structurally, the B. halodurans enzyme resembled the Mycobacterium tuberculosis enzyme the most. An investigation of sequenced genomes from other species of the genus Bacillus revealed that not only the genome of B. halodurans but also the genomes of Bacillus pseudofirmus, Bacillus thuringiensis, Bacillus hemicellulosilyticus, Bacillus marmarensis, Bacillus cereus, and Bacillus megaterium encode both the dCMP deaminase and the DCD:DUT enzymes. In addition, eight dcdB homologs from Bacillus species within the genus for which the whole genome has not yet been sequenced were registered in the NCBI Entrez database.


    Organizational Affiliation

    Metabolic Signaling and Regulation Group, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.,Department of Biology, Section for Biomolecular Sciences, University of Copenhagen, Copenhagen, Denmark ph@kemi.dtu.dk willemoes@bio.ku.dk.,Department of Chemistry, Technical University of Denmark, Lyngby, Denmark.,Department of Biology, Section for Biomolecular Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Chemistry, Technical University of Denmark, Lyngby, Denmark ph@kemi.dtu.dk willemoes@bio.ku.dk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Deoxycytidine triphosphate deaminase
A, C, E, B, D, F
177Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)Mutation(s): 0 
Gene Names: dcd (dcdB)
EC: 3.5.4.30
Find proteins for Q9KFV3 (Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Go to UniProtKB:  Q9KFV3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TTP
Query on TTP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 92.720α = 90.00
b = 55.630β = 97.36
c = 95.600γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
MOLREPphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-05-06
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Data collection