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 

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
ELP3 family, ELP3 familyA450Dehalococcoides mccartyi BTF08Mutation(s): 0 
Gene Names: btf_573
EC: 2.3.1
UniProt
Find proteins for A0A1C7D1B7 (Dehalococcoides mccartyi (strain CBDB1))
Explore A0A1C7D1B7 
Go to UniProtKB:  A0A1C7D1B7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCA
Query on DCA

Download Ideal Coordinates CCD File 
B [auth A]DESULFO-COENZYME A
C21 H36 N7 O16 P3
ILWZMFJBPIYQKW-IBOSZNHHSA-N
 Ligand Interaction
FES
Query on FES

Download Ideal Coordinates CCD File 
C [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
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

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
PolandUMO-2015/19/B/NZ1/00343

Revision History  (Full details and data files)

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