Crystal structure of Tryptophanyl-tRNA synthetase (EC (Tryptophan-tRNA ligase)(TrpRS) (tm0492) from THERMOTOGA MARITIMA at 2.50 A resolution

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Structure of a tryptophanyl-tRNA synthetase containing an iron-sulfur cluster.

Han, G.W.Yang, X.L.McMullan, D.Chong, Y.E.Krishna, S.S.Rife, C.L.Weekes, D.Brittain, S.M.Abdubek, P.Ambing, E.Astakhova, T.Axelrod, H.L.Carlton, D.Caruthers, J.Chiu, H.J.Clayton, T.Duan, L.Feuerhelm, J.Grant, J.C.Grzechnik, S.K.Jaroszewski, L.Jin, K.K.Klock, H.E.Knuth, M.W.Kumar, A.Marciano, D.Miller, M.D.Morse, A.T.Nigoghossian, E.Okach, L.Paulsen, J.Reyes, R.van den Bedem, H.White, A.Wolf, G.Xu, Q.Hodgson, K.O.Wooley, J.Deacon, A.M.Godzik, A.Lesley, S.A.Elsliger, M.A.Schimmel, P.Wilson, I.A.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1326-1334

  • DOI: https://doi.org/10.1107/S1744309110037619
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A novel aminoacyl-tRNA synthetase that contains an iron-sulfur cluster in the tRNA anticodon-binding region and efficiently charges tRNA with tryptophan has been found in Thermotoga maritima. The crystal structure of TmTrpRS (tryptophanyl-tRNA synthetase; TrpRS; EC reveals an iron-sulfur [4Fe-4S] cluster bound to the tRNA anticodon-binding (TAB) domain and an L-tryptophan ligand in the active site. None of the other T. maritima aminoacyl-tRNA synthetases (AARSs) contain this [4Fe-4S] cluster-binding motif (C-x₂₂-C-x₆-C-x₂-C). It is speculated that the iron-sulfur cluster contributes to the stability of TmTrpRS and could play a role in the recognition of the anticodon.

  • Organizational Affiliation

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptophanyl-tRNA synthetase340Thermotoga maritimaMutation(s): 0 
Gene Names: trpS
Find proteins for Q9WYW2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WYW2 
Go to UniProtKB:  Q9WYW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WYW2
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.89α = 90
b = 152.73β = 90
c = 53.07γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2017-10-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-01-25
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-04-03
    Changes: Data collection, Refinement description