2ZPA

Crystal Structure of tRNA(Met) Cytidine Acetyltransferase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.235 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon

Chimnaronk, S., Suzuki, T., Manita, T., Ikeuchi, Y., Yao, M., Suzuki, T., Tanaka, I.

(2009) EMBO J 28: 1362-1373

  • DOI: 10.1038/emboj.2009.69
  • Primary Citation of Related Structures:  
    2ZPA

  • PubMed Abstract: 

    • Post-transcriptional RNA modifications in the anticodon of transfer RNAs frequently contribute to the high fidelity of protein synthesis. In eubacteria, two genome-encoded transfer RNA (tRNA) species bear the same CAU sequence as the anticodons, which are differentiated by modified cytidines at the wobble positions ...

    Post-transcriptional RNA modifications in the anticodon of transfer RNAs frequently contribute to the high fidelity of protein synthesis. In eubacteria, two genome-encoded transfer RNA (tRNA) species bear the same CAU sequence as the anticodons, which are differentiated by modified cytidines at the wobble positions. The elongator tRNA(Met) accepts an acetyl moiety at the wobble base to form N(4)-acetylcytidine (ac(4)C): an inherent modification ensures precise decoding of the AUG codon by strengthening C-G base-pair interaction and concurrently preventing misreading of the near cognate AUA codon. We have determined the crystal structure of tRNA(Met) cytidine acetyltransferase (TmcA) from Escherichia coli complexed with two natural ligands, acetyl-CoA and ADP, at 2.35 A resolution. The structure unexpectedly reveals an idiosyncratic RNA helicase module fused with a GCN5-related N-acetyltransferase (GNAT) fold, which intimately cross-interact. Taken together with the biochemical evidence, we further unravelled the function of acetyl-CoA as an enzyme-activating switch, and propose that an RNA helicase motor driven by ATP hydrolysis is used to deliver the wobble base to the active centre of the GNAT domain.

    Organizational Affiliation: 

    Faculty of Advanced Life Sciences, Hokkaido University, Sapporo, Japan.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized protein ypfIA, B671Escherichia coli K-12Mutation(s): 0 
Gene Names: tmcA, ypfI, b2474, JW2459
EC: 2.3.1 (PDB Primary Data), 2.3.1.193 (UniProt)
UniProt
Find proteins for P76562 (Escherichia coli (strain K12))
Explore P76562 
Go to UniProtKB:  P76562
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76562
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACO
Query on ACO
Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]		ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N		 Ligand Interaction
ADP
Query on ADP
Download Ideal Coordinates CCD File 
D [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.298α = 90
b = 100.99β = 90
c = 263.116γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance