6IA6

Crystal structure of the bacterial Dehalococcoides mccartyi Elp3 with desulfo-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase.

Lin, T.Y.Abbassi, N.E.H.Zakrzewski, K.Chramiec-Glabik, A.Jemiola-Rzeminska, M.Rozycki, J.Glatt, S.

(2019) Nat Commun 10: 625-625

  • DOI: https://doi.org/10.1038/s41467-019-08579-2
  • Primary Citation of Related Structures:  
    6IA6, 6IA8, 6IAD, 6IAZ

  • PubMed Abstract: 

    The Elongator complex catalyzes posttranscriptional tRNA modifications by attaching carboxy-methyl (cm 5 ) moieties to uridine bases located in the wobble position. The catalytic subunit Elp3 is highly conserved and harbors two individual subdomains, a radical S-adenosyl methionine (rSAM) and a lysine acetyltransferase (KAT) domain. The details of its modification reaction cycle and particularly the substrate specificity of its KAT domain remain elusive. Here, we present the co-crystal structure of bacterial Elp3 (DmcElp3) bound to an acetyl-CoA analog and compare it to the structure of a monomeric archaeal Elp3 from Methanocaldococcus infernus (MinElp3). Furthermore, we identify crucial active site residues, confirm the importance of the extended N-terminus for substrate recognition and uncover the specific induction of acetyl-CoA hydrolysis by different tRNA species. In summary, our results establish the clinically relevant Elongator subunit as a non-canonical acetyltransferase and genuine tRNA modification enzyme.


  • Organizational Affiliation

    Max Planck Laboratory, Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, 30-387, Poland. sebastian.glatt@uj.edu.pl.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ELP3 family, ELP3 family450Dehalococcoides mccartyi BTF08Mutation(s): 0 
Gene Names: btf_573
UniProt
Find proteins for A0A1C7D1B7 (Dehalococcoides mccartyi (strain CBDB1))
Explore A0A1C7D1B7 
Go to UniProtKB:  A0A1C7D1B7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C7D1B7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.54α = 90
b = 160.74β = 90
c = 92.99γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
PolandHoming/2016-2/14
PolandUMO-2015/19/B/NZ1/00343

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description