5Y0T

Crystal structure of Thermotoga maritima TmcAL bound with alpha-thio ATP(Form II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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
Thermotoga maritima TmcAL
A, B, C, D
425Thermotoga maritimaMutation(s): 0 
EC: 6.3.4
UniProt
Find proteins for Q9X1K1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X1K1 
Go to UniProtKB:  Q9X1K1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X1K1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TAT
Query on TAT

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
M [auth C],
P [auth D]
ADENOSINE-5'-RP-ALPHA-THIO-TRIPHOSPHATE
C10 H16 N5 O12 P3 S
ROYJKVPBJVNHCQ-AJBXOXQOSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
R [auth D]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
J [auth B]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
N [auth C],
O [auth C],
Q [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
CSD
Query on CSD
A, B, C, D
L-PEPTIDE LINKINGC3 H7 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.618α = 90
b = 97.813β = 99.28
c = 144.605γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary