Crystal structure of Thermotoga maritima holo RimO in complex with pentasulfide, Northeast Structural Genomics Consortium Target VR77

Experimental Data Snapshot

  • Resolution: 3.30 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 

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Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases.

Forouhar, F.Arragain, S.Atta, M.Gambarelli, S.Mouesca, J.M.Hussain, M.Xiao, R.Kieffer-Jaquinod, S.Seetharaman, J.Acton, T.B.Montelione, G.T.Mulliez, E.Hunt, J.F.Fontecave, M.

(2013) Nat Chem Biol 9: 333-338

  • DOI: https://doi.org/10.1038/nchembio.1229
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    How living organisms create carbon-sulfur bonds during the biosynthesis of critical sulfur-containing compounds is still poorly understood. The methylthiotransferases MiaB and RimO catalyze sulfur insertion into tRNAs and ribosomal protein S12, respectively. Both belong to a subgroup of radical-S-adenosylmethionine (radical-SAM) enzymes that bear two [4Fe-4S] clusters. One cluster binds S-adenosylmethionine and generates an Ado• radical via a well-established mechanism. However, the precise role of the second cluster is unclear. For some sulfur-inserting radical-SAM enzymes, this cluster has been proposed to act as a sacrificial source of sulfur for the reaction. In this paper, we report parallel enzymological, spectroscopic and crystallographic investigations of RimO and MiaB, which provide what is to our knowledge the first evidence that these enzymes are true catalysts and support a new sulfation mechanism involving activation of an exogenous sulfur cosubstrate at an exchangeable coordination site on the second cluster, which remains intact during the reaction.

  • Organizational Affiliation

    Northeast Structural Genomics Consortium, New York, New York, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S12 methylthiotransferase RimO
A, B
438Thermotoga maritimaMutation(s): 0 
Gene Names: rimOTM1862TM_1862
EC: 2 (PDB Primary Data), (UniProt)
Find proteins for Q9X2H6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X2H6 
Go to UniProtKB:  Q9X2H6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X2H6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FS5

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
Fe8 S13
Experimental Data & Validation

Experimental Data

  • Resolution: 3.30 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.721α = 90
b = 86.948β = 90
c = 172.795γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description