2QGQ

Crystal structure of TM_1862 from Thermotoga maritima. Northeast Structural Genomics Consortium target VR77


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Post-translational Modification of Ribosomal Proteins: STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF RimO FROM THERMOTOGA MARITIMA, A RADICAL S-ADENOSYLMETHIONINE METHYLTHIOTRANSFERASE.

Arragain, S.Garcia-Serres, R.Blondin, G.Douki, T.Clemancey, M.Latour, J.M.Forouhar, F.Neely, H.Montelione, G.T.Hunt, J.F.Mulliez, E.Fontecave, M.Atta, M.

(2010) J.Biol.Chem. 285: 5792-5801

  • DOI: 10.1074/jbc.M109.065516

  • PubMed Abstract: 
  • Post-translational modifications of ribosomal proteins are important for the accuracy of the decoding machinery. A recent in vivo study has shown that the rimO gene is involved in generation of the 3-methylthio derivative of residue Asp-89 in ribosom ...

    Post-translational modifications of ribosomal proteins are important for the accuracy of the decoding machinery. A recent in vivo study has shown that the rimO gene is involved in generation of the 3-methylthio derivative of residue Asp-89 in ribosomal protein S12 (Anton, B. P., Saleh, L., Benner, J. S., Raleigh, E. A., Kasif, S., and Roberts, R. J. (2008) Proc. Natl. Acad. Sci. U. S. A. 105, 1826-1831). This reaction is formally identical to that catalyzed by MiaB on the C2 of adenosine 37 near the anticodon of several tRNAs. We present spectroscopic evidence that Thermotoga maritima RimO, like MiaB, contains two [4Fe-4S] centers, one presumably bound to three invariant cysteines in the central radical S-adenosylmethionine (AdoMet) domain and the other to three invariant cysteines in the N-terminal UPF0004 domain. We demonstrate that holo-RimO can specifically methylthiolate the aspartate residue of a 20-mer peptide derived from S12, yielding a mixture of mono- and bismethylthio derivatives. Finally, we present the 2.0 A crystal structure of the central radical AdoMet and the C-terminal TRAM (tRNA methyltransferase 2 and MiaB) domains in apo-RimO. Although the core of the open triose-phosphate isomerase (TIM) barrel of the radical AdoMet domain was conserved, RimO showed differences in domain organization compared with other radical AdoMet enzymes. The unusually acidic TRAM domain, likely to bind the basic S12 protein, is located at the distal edge of the radical AdoMet domain. The basic S12 protein substrate is likely to bind RimO through interactions with both the TRAM domain and the concave surface of the incomplete TIM barrel. These biophysical results provide a foundation for understanding the mechanism of methylthioation by radical AdoMet enzymes in the MiaB/RimO family.


    Organizational Affiliation

    Institut de Recherches en Technologie et Sciences pour le Vivant-Laboratoire de Chimie et Biologie des Métaux (iRTSV-LCBM), UMR 5249, CEA-CNRS-UJF, Commissariat à l'Energie Atomique Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 09, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein TM_1862
A, B, C, D, E, F, G, H
304Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Gene Names: rimO
EC: 2.8.4.4
Find proteins for Q9X2H6 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9X2H6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CXS
Query on CXS

Download SDF File 
Download CCD File 
A, B, D, F
3-CYCLOHEXYL-1-PROPYLSULFONIC ACID
C9 H19 N O3 S
PJWWRFATQTVXHA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.212 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 88.620α = 89.98
b = 88.649β = 90.03
c = 96.039γ = 89.91
Software Package:
Software NamePurpose
HKL-2000data scaling
SnBphasing
CNSrefinement
HKL-2000data reduction
RESOLVEphasing
ADSCdata collection
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2007-07-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description