1VK8

CRYSTAL STRUCTURE OF A PUTATIVE THIAMINE BIOSYNTHESIS/SALVAGE PROTEIN (TM0486) FROM THERMOTOGA MARITIMA AT 1.80 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.142 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

TM0486 from the hyperthermophilic anaerobe Thermotoga maritima is a thiamin-binding protein involved in response of the cell to oxidative conditions.

Dermoun, Z.Foulon, A.Miller, M.D.Harrington, D.J.Deacon, A.M.Sebban-Kreuzer, C.Roche, P.Lafitte, D.Bornet, O.Wilson, I.A.Dolla, A.

(2010) J.Mol.Biol. 400: 463-476

  • DOI: 10.1016/j.jmb.2010.05.014

  • PubMed Abstract: 
  • The COG database was used for a comparative genome analysis with genomes from anaerobic and aerobic microorganisms with the aim of identifying proteins specific to the anaerobic way of life. A total of 33 COGs were identified, five of which correspon ...

    The COG database was used for a comparative genome analysis with genomes from anaerobic and aerobic microorganisms with the aim of identifying proteins specific to the anaerobic way of life. A total of 33 COGs were identified, five of which correspond to proteins of unknown function. We focused our study on TM0486 from Thermotoga maritima, which belongs to one of these COGs of unknown function, namely COG0011. The crystal structure of the protein was determined at 2 A resolution. The structure adopts a beta alpha beta beta alpha beta ferredoxin-like fold and assembles as a homotetramer. The structure also revealed the presence of a pocket in each monomer that bound an unidentified ligand. NMR and calorimetry revealed that TM0486 specifically bound thiamin with a K(d) of 1.58 microM, but not hydroxymethyl pyrimidine (HMP), which has been implicated as a potential ligand. We demonstrated that the TM0486 gene belongs to the same multicistronic unit as TM0483, TM0484 and TM0485. Although these three genes have been assigned to the transport of HMP, with TM0484 being the periplasmic thiamin/HMP-binding protein and TM0485 and TM0483 the transmembrane and the ATPase components, respectively, our results led us to conclude that this operon encodes an ABC transporter dedicated to thiamin, with TM0486 transporting charged thiamin in the cytoplasm. Given that this transcriptional unit was up-regulated when T. maritima was exposed to oxidative conditions, we propose that, by chelating cytoplasmic thiamin, TM0486 and, by extension, proteins belonging to COG0011 are involved in the response mechanism to stress that could arise during aerobic conditions.


    Organizational Affiliation

    IMR-CNRS, IFR88, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France. dermoun@ibsm.cnrs-mrs.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
hypothetical protein TM0486
A, B, C, D
106Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)N/A
Find proteins for Q9WYV6 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9WYV6
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 47.646α = 73.80
b = 47.650β = 62.90
c = 49.608γ = 73.62
Software Package:
Software NamePurpose
CCP4data scaling
SOLVEphasing
RESOLVEmodel building
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
RESOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-05-18
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance