5MKO

[2Fe-2S] cluster containing TtuA in complex with AMP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
FES
Query on FES

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
H [auth B],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.86α = 90
b = 72.32β = 90
c = 128.28γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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