6IA6

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

Summary for 6IA6

• Entry DOI: 10.2210/pdb6ia6/pdb
• Descriptor: ELP3 family, ELP3 family, DESULFO-COENZYME A, FE2/S2 (INORGANIC) CLUSTER, ... (4 entities in total)
• Functional Keywords: trna binding, elongator complex, non-canonical acetyltransferase, acetyl-coa hydrolysis, transferase
• Biological source: Dehalococcoides mccartyi BTF08
• Total number of polymer chains: 1
• Total formula weight: 50947.01

Authors

Lin, T.Y.,Glatt, S. (deposition date: 2018-11-26, release date: 2019-02-20, Last modification date: 2024-01-24)

Primary citation

Lin, T.Y.,Abbassi, N.E.H.,Zakrzewski, K.,Chramiec-Glabik, A.,Jemiola-Rzeminska, M.,Rozycki, J.,Glatt, S.
The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase.
Nat Commun, 10:625-625, 2019

PubMed Abstract: The Elongator complex catalyzes posttranscriptional tRNA modifications by attaching carboxy-methyl (cm) 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.

PubMed: 30733442
DOI: 10.1038/s41467-019-08579-2

Experimental method

X-RAY DIFFRACTION (2.7 Å)