2G36

Crystal structure of Tryptophanyl-tRNA synthetase (EC 6.1.1.2) (Tryptophan-tRNA ligase)(TrpRS) (tm0492) from THERMOTOGA MARITIMA at 2.50 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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 66: 1326-1334

  • DOI: 10.1107/S1744309110037619

  • 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 synthe ...

    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 6.1.1.2) 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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tryptophanyl-tRNA synthetase
A
340Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Gene Names: trpS
EC: 6.1.1.2
Find proteins for Q9WYW2 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9WYW2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
TRP
Query on TRP

Download SDF File 
Download CCD File 
A
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 122.890α = 90.00
b = 152.730β = 90.00
c = 53.070γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
MOLREPphasing
XDSdata reduction
XSCALEdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2017-10-25
    Type: Author supporting evidence