6IAZ

The archaeal Methanocaldococcus infernus Elp3 with N-terminus deletion (1-46)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.0 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: 10.1038/s41467-019-08579-2
  • Primary Citation of Related Structures:  
    6IAD, 6IA6, 6IA8, 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 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone acetyltransferase, ELP3 familyA492Methanocaldococcus infernusMutation(s): 0 
Gene Names: Metin_0452
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt
Find proteins for D5VRB9 (Methanocaldococcus infernus (strain DSM 11812 / JCM 15783 / ME))
Explore D5VRB9 
Go to UniProtKB:  D5VRB9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.35α = 90
b = 63.35β = 90
c = 250.06γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-11-28 
  • Released Date: 2019-02-20 
  • Deposition Author(s): Lin, T.Y., Glatt, S.

Funding OrganizationLocationGrant Number
PolandHoming/2016-2/14
Polish National Science CentrePolandUMO-2015/19/B/NZ1/00343
PolandTEAM TECH CORE FACILITY/2017-4/6

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release