5MKP | pdb_00005mkp

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

• PDB DOI: https://doi.org/10.2210/pdb5MKP/pdb

• Classification: RNA
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-05 Released: 2017-06-14 
• Deposition Author(s): Arragain, S., Bimai, O., Legrand, P., Golinelli-Pimpaneau, B.
• Funding Organization(s): LABEX, French National Research Agency

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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), 0.194 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

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

• PubMed: 28655838 
• DOI: https://doi.org/10.1073/pnas.1700902114
• Primary Citation 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.

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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.
SOLEIL Synchrotron, L'Orme des Merisiers, 91198 Gif-sur-Yvette, France.
University of Grenoble Alpes, Commissariat à l'Energie Atomique, Institut Nanosciences et Cryogénie, Systèmes Moléculaires et Nanomatériaux pour l'Energie et la Santé, F-38054 Grenoble, France.
CNRS Institut de Recherche Renard, Chimie-ParisTech, 75005 Paris, France.
Paris Sciences et Lettres Research University, Chimie-ParisTech, Institut de Recherche de Chimie-Paris, 75005 Paris, France.
University of Grenoble Alpes, Commissariat à l'Energie Atomique, Direction de Recherche Fondamentale, Institut de Biosciences et Biotechnologies de Grenoble, Laboratoire Chimie et Biologie des Métaux, Unité Mixte de Recherche 5249, F-38000 Grenoble, France.
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; [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 36.44 kDa 
• Atom Count: 2,602 
• Modeled Residue Count: 307 
• Deposited Residue Count: 313 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PH0300	A	313	Pyrococcus horikoshii OT3	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q46	D [auth A]	Fe4 H S5 Fe4 H S5 IBBAXWHZAAYJDG-UHFFFAOYSA-M
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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), 0.194 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.12	α = 90
b = 70.12	β = 90
c = 127.9	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): Arragain, S., Bimai, O., Legrand, P., Golinelli-Pimpaneau, B.

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Funding Organization	Location	Grant Number
LABEX	France	LABEX DYNAMO
French National Research Agency	France	ANR-11-LABX-0011

Revision History  

• 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