8VTZ | pdb_00008vtz

Crystal structure of Aquifex aeolicus Trbp111

• PDB DOI: https://doi.org/10.2210/pdb8VTZ/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-01-27 Released: 2024-08-07 
• Deposition Author(s): Umuhire Juru, A., Zhang, J.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Structural basis of tRNA recognition by the widespread OB fold.

Umuhire Juru, A., Ghirlando, R., Zhang, J.

(2024) Nat Commun 15: 6385-6385

• PubMed: 39075051 
• DOI: https://doi.org/10.1038/s41467-024-50730-1
• Primary Citation Related Structures: 
  8VTZ, 8VU0


• PubMed Abstract: 
  

  The widespread oligonucleotide/oligosaccharide-binding (OB)-fold recognizes diverse substrates from sugars to nucleic acids and proteins, and plays key roles in genome maintenance, transcription, translation, and tRNA metabolism. OB-containing bacterial Trbp and yeast Arc1p proteins are thought to recognize the tRNA elbow or anticodon regions. Here we report a 2.6 Å co-crystal structure of Aquifex aeolicus Trbp111 bound to tRNA ^Ile , which reveals that Trbp recognizes tRNAs solely by capturing their 3' ends. Structural, mutational, and biophysical analyses show that the Trbp/EMAPII-like OB fold precisely recognizes the single-stranded structure, 3' terminal location, and specific sequence of the 3' CA dinucleotide - a universal feature of mature tRNAs. Arc1p supplements its OB - tRNA 3' end interaction with additional contacts that involve an adjacent basic region and the tRNA body. This study uncovers a previously unrecognized mode of tRNA recognition by an ancient protein fold, and provides insights into protein-mediated tRNA aminoacylation, folding, localization, trafficking, and piracy.

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Organizational Affiliation: 
• Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 24.63 kDa 
• Atom Count: 1,779 
• Modeled Residue Count: 226 
• Deposited Residue Count: 226 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionyl-tRNA synthetase beta subunit	A, B	113	Aquifex aeolicus	Mutation(s): 0  Gene Names: metG', aq_422 EC: 6.1.1.10
UniProt
Find proteins for O66738 (Aquifex aeolicus (strain VF5)) Explore O66738  Go to UniProtKB:  O66738

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.002	α = 90
b = 82.221	β = 90
c = 88.882	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Umuhire Juru, A., Zhang, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	ZIADK075136

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release