5Y0N

Crystal structure of Bacillus subtilis TmcAL bound with ATP (SeMet derivative)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis.

Taniguchi, T.Miyauchi, K.Sakaguchi, Y.Yamashita, S.Soma, A.Tomita, K.Suzuki, T.

(2018) Nat Chem Biol 14: 1010-1020

  • DOI: https://doi.org/10.1038/s41589-018-0119-z
  • Primary Citation of Related Structures:  
    5Y0N, 5Y0O, 5Y0P, 5Y0Q, 5Y0R, 5Y0S, 5Y0T

  • PubMed Abstract: 

    Modification of tRNA anticodons plays a critical role in ensuring accurate translation. N 4 -acetylcytidine (ac 4 C) is present at the anticodon first position (position 34) of bacterial elongator tRNA Met . Herein, we identified Bacillus subtilis ylbM (renamed tmcAL) as a novel gene responsible for ac 4 C34 formation. Unlike general acetyltransferases that use acetyl-CoA, TmcAL activates an acetate ion to form acetyladenylate and then catalyzes ac 4 C34 formation through a mechanism similar to tRNA aminoacylation. The crystal structure of TmcAL with an ATP analog reveals the molecular basis of ac 4 C34 formation. The ΔtmcAL strain displayed a cold-sensitive phenotype and a strong genetic interaction with tilS that encodes the enzyme responsible for synthesizing lysidine (L) at position 34 of tRNA Ile to facilitate AUA decoding. Mistranslation of the AUA codon as Met in the ΔtmcAL strain upon tilS repression suggests that ac 4 C34 modification of tRNA Met and L34 modification of tRNA Ile act cooperatively to prevent misdecoding of the AUA codon.


  • Organizational Affiliation

    Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UPF0348 protein B4417_3650
A, B
435Bacillus subtilisMutation(s): 0 
Gene Names: B4417_3650
UniProt
Find proteins for O34513 (Bacillus subtilis (strain 168))
Explore O34513 
Go to UniProtKB:  O34513
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO34513
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.037α = 90
b = 68.021β = 90
c = 209.952γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPSJapan26113002

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references, Structure summary