6IAD

Apo crystal structure of archaeal Methanocaldococcus infernus Elp3 (del1-54)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone acetyltransferase, ELP3 family
A
483Methanocaldococcus infernus MEMutation(s): 0 
Gene Names: Metin_0452
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
Find proteins for D5VRB9 (Methanocaldococcus infernus (strain DSM 11812 / JCM 15783 / ME))
Go to UniProtKB:  D5VRB9
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.198 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.97α = 90
b = 62.97β = 90
c = 248.25γ = 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: 2018-11-26 
  • 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

Revision History 

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