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6iaz

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

Structural highlights

6iaz is a 1 chain structure with sequence from Methanocaldococcus infernus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.901Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ELP3_METIM tRNA uridine(34) acetyltransferase, which mediates formation of carboxymethyluridine in the wobble base at position 34 in tRNAs (PubMed:25151136, PubMed:30733442). The proposed mechanism is the following: (i) recruits S-adenosyl-L-methionine and cleaves it to generate a 5'-deoxyadenosine radical (5'-dA) in the radical S-adenosyl-L-methionine (rSAM) region, (ii) hydrolyzes acetyl-CoA in the N-acetyltransferase domain and (iii) an acetyl radical is formed by the products of the two domains and (iv) is transferred onto the C5 position of uridine(34) in the bound tRNA molecule (PubMed:25151136). Does not show protein lysine acetyltransferase activity (PubMed:30733442).^[1] ^[2]

Publication Abstract from PubMed

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.

The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase.,Lin TY, Abbassi NEH, Zakrzewski K, Chramiec-Glabik A, Jemiola-Rzeminska M, Rozycki J, Glatt S Nat Commun. 2019 Feb 7;10(1):625. doi: 10.1038/s41467-019-08579-2. PMID:30733442^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Selvadurai K, Wang P, Seimetz J, Huang RH. Archaeal Elp3 catalyzes tRNA wobble uridine modification at C5 via a radical mechanism. Nat Chem Biol. 2014 Oct;10(10):810-2. PMID:25151136 doi:10.1038/nchembio.1610
↑ Lin TY, Abbassi NEH, Zakrzewski K, Chramiec-Glabik A, Jemiola-Rzeminska M, Rozycki J, Glatt S. The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase. Nat Commun. 2019 Feb 7;10(1):625. doi: 10.1038/s41467-019-08579-2. PMID:30733442 doi:http://dx.doi.org/10.1038/s41467-019-08579-2
↑ Lin TY, Abbassi NEH, Zakrzewski K, Chramiec-Glabik A, Jemiola-Rzeminska M, Rozycki J, Glatt S. The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase. Nat Commun. 2019 Feb 7;10(1):625. doi: 10.1038/s41467-019-08579-2. PMID:30733442 doi:http://dx.doi.org/10.1038/s41467-019-08579-2