5MKP | pdb_00005mkp

Non redox thiolation in transfer RNAs occuring via sulfur activation by a [4Fe-4S] cluster


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.245 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.6 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
PH0300313Pyrococcus horikoshii OT3Mutation(s): 0 
Gene Names: PH0300
EC: 2.8.1
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: 2.50 Å
  • R-Value Free:  0.245 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.12α = 90
b = 70.12β = 90
c = 127.9γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LABEXFranceLABEX 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, Structure summary
  • 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: 2018-01-31
    Changes: Database references
  • Version 1.6: 2024-01-17
    Changes: Data collection, Database references, Refinement description