5MKQ

TtuA enzyme containing a [4Fe-4S]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Nonredox thiolation in tRNA occurring via sulfur activation by a [4Fe-4S] cluster.

Arragain, S.Bimai, O.Legrand, P.Caillat, S.Ravanat, J.L.Touati, N.Binet, L.Atta, M.Fontecave, M.Golinelli-Pimpaneau, B.

(2017) Proc Natl Acad Sci U S A 114: 7355-7360

  • DOI: https://doi.org/10.1073/pnas.1700902114
  • Primary Citation of Related Structures:  
    5MKO, 5MKP, 5MKQ

  • PubMed Abstract: 

    Sulfur is present in several nucleosides within tRNAs. In particular, thiolation of the universally conserved methyl-uridine at position 54 stabilizes tRNAs from thermophilic bacteria and hyperthermophilic archaea and is required for growth at high temperature. The simple nonredox substitution of the C2-uridine carbonyl oxygen by sulfur is catalyzed by tRNA thiouridine synthetases called TtuA. Spectroscopic, enzymatic, and structural studies indicate that TtuA carries a catalytically essential [4Fe-4S] cluster and requires ATP for activity. A series of crystal structures shows that ( i ) the cluster is ligated by only three cysteines that are fully conserved, allowing the fourth unique iron to bind a small ligand, such as exogenous sulfide, and ( ii ) the ATP binding site, localized thanks to a protein-bound AMP molecule, a reaction product, is adjacent to the cluster. A mechanism for tRNA sulfuration is suggested, in which the unique iron of the catalytic cluster serves to bind exogenous sulfide, thus acting as a sulfur carrier.


  • Organizational Affiliation

    Laboratoire de Chimie des Processus Biologiques, Unité Mixte de Recherche 8229 CNRS, Collège de France, Université Pierre et Marie Curie, 75231 Paris cedex 05, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TtuA PH0300
A, B
313Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: PH0300
UniProt
Find proteins for O58038 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O58038 
Go to UniProtKB:  O58038
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO58038
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.45α = 90
b = 72.19β = 90
c = 127.95γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LABEX-DYNAMOFranceLABEX-DYNAMO
French National Research AgencyFranceANR-11-LABX-0011

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2017-07-12
    Changes: Database references
  • Version 1.3: 2017-07-19
    Changes: Database references
  • Version 1.4: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.5: 2024-01-17
    Changes: Data collection, Database references, Refinement description