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Name ^help_outline acetyl-CoA Identifier CHEBI:57288 (Beilstein: 8468140) ^help_outline Charge -4 Formula C23H34N7O17P3S InChIKey^help_outline ZSLZBFCDCINBPY-ZSJPKINUSA-J SMILES^help_outline CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)COP([O-])(=O)OP([O-])(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP([O-])([O-])=O)n1cnc2c(N)ncnc12 2D coordinates Mol file for the small molecule Search links Involved in 352 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline H₂O Identifier CHEBI:15377 (Beilstein: 3587155; CAS: 7732-18-5) ^help_outline Charge 0 Formula H2O InChIKey^help_outline XLYOFNOQVPJJNP-UHFFFAOYSA-N SMILES^help_outline [H]O[H] 2D coordinates Mol file for the small molecule Search links Involved in 6,204 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline S-adenosyl-L-methionine Identifier CHEBI:59789 Charge 1 Formula C15H23N6O5S InChIKey^help_outline MEFKEPWMEQBLKI-AIRLBKTGSA-O SMILES^help_outline C[S+](CC[C@H]([NH3+])C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1cnc2c(N)ncnc12 2D coordinates Mol file for the small molecule Search links Involved in 868 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name^help_outline uridine³⁴ in tRNA Identifier RHEA-COMP:11727 Reactive part ^help_outline
- Name ^help_outline UMP residue Identifier CHEBI:65315 Charge -1 Formula C9H10N2O8P Position^help_outline 34 SMILES^help_outline C1=CC(NC(N1[C@@H]2O[C@H](COP(*)(=O)[O-])[C@H]([C@H]2O)O*)=O)=O 2D coordinates Mol file for the small molecule Search links Involved in 73 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Search links Involved in 3 reaction(s) Find proteins in UniProtKB for this molecule
Name ^help_outline 5'-deoxyadenosine Identifier CHEBI:17319 (CAS: 4754-39-6) ^help_outline Charge 0 Formula C10H13N5O3 InChIKey^help_outline XGYIMTFOTBMPFP-KQYNXXCUSA-N SMILES^help_outline C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n1cnc2c(N)ncnc12 2D coordinates Mol file for the small molecule Search links Involved in 69 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name^help_outline 5-(carboxymethyl)uridine³⁴ in tRNA Identifier RHEA-COMP:10407 Reactive part ^help_outline
- Name ^help_outline carboxymethyluridine 5'-phosphate residue Identifier CHEBI:74882 Charge -2 Formula C11H11N2O10P Position^help_outline 34 SMILES^help_outline C1=C(C(NC(N1[C@@H]2O[C@H](COP(*)(=O)[O-])[C@H]([C@H]2O)O*)=O)=O)CC([O-])=O 2D coordinates Mol file for the small molecule Search links Involved in 2 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Search links Involved in 2 reaction(s) Find proteins in UniProtKB for this molecule
Name ^help_outline CoA Identifier CHEBI:57287 (Beilstein: 11604429) ^help_outline Charge -4 Formula C21H32N7O16P3S InChIKey^help_outline RGJOEKWQDUBAIZ-IBOSZNHHSA-J SMILES^help_outline CC(C)(COP([O-])(=O)OP([O-])(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP([O-])([O-])=O)n1cnc2c(N)ncnc12)[C@@H](O)C(=O)NCCC(=O)NCCS 2D coordinates Mol file for the small molecule Search links Involved in 1,500 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline H⁺ Identifier CHEBI:15378 Charge 1 Formula H InChIKey^help_outline GPRLSGONYQIRFK-UHFFFAOYSA-N SMILES^help_outline [H+] 2D coordinates Mol file for the small molecule Search links Involved in 9,431 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Name ^help_outline L-methionine Identifier CHEBI:57844 Charge 0 Formula C5H11NO2S InChIKey^help_outline FFEARJCKVFRZRR-BYPYZUCNSA-N SMILES^help_outline CSCC[C@H]([NH3+])C([O-])=O 2D coordinates Mol file for the small molecule Search links Involved in 121 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule

Cross-references

	RHEA:61020	RHEA:61021	RHEA:61022	RHEA:61023
Reaction direction	undefined	left-to-right	right-to-left	bidirectional
UniProtKB ^help_outline	7,362 proteins	7,256 proteins
EC numbers ^help_outline	2.3.1.311
Gene Ontology ^help_outline	GO:0106261
MetaCyc ^help_outline		RXN-23599

Publications

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.

The Elongator complex catalyzes posttranscriptional tRNA modifications by attaching carboxy-methyl (cm<sup>5</sup>) 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) ... >> More

The Elongator complex catalyzes posttranscriptional tRNA modifications by attaching carboxy-methyl (cm<sup>5</sup>) 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. << Less

Nat. Commun. 10:625-625(2019) [PubMed] [EuropePMC]
Structural basis for tRNA modification by Elp3 from Dehalococcoides mccartyi.

Glatt S., Zabel R., Kolaj-Robin O., Onuma O.F., Baudin F., Graziadei A., Taverniti V., Lin T.Y., Baymann F., Seraphin B., Breunig K.D., Mueller C.W.

During translation elongation, decoding is based on the recognition of codons by corresponding tRNA anticodon triplets. Molecular mechanisms that regulate global protein synthesis via specific base modifications in tRNA anticodons are receiving increasing attention. The conserved eukaryotic Elonga ... >> More

During translation elongation, decoding is based on the recognition of codons by corresponding tRNA anticodon triplets. Molecular mechanisms that regulate global protein synthesis via specific base modifications in tRNA anticodons are receiving increasing attention. The conserved eukaryotic Elongator complex specifically modifies uridines located in the wobble base position of tRNAs. Mutations in Elongator subunits are associated with certain neurodegenerative diseases and cancer. Here we present the crystal structure of D. mccartyi Elp3 (DmcElp3) at 2.15-Å resolution. Our results reveal an unexpected arrangement of Elp3 lysine acetyltransferase (KAT) and radical S-adenosyl methionine (SAM) domains, which share a large interface and form a composite active site and tRNA-binding pocket, with an iron-sulfur cluster located in the dimerization interface of two DmcElp3 molecules. Structure-guided mutagenesis studies of yeast Elp3 confirmed the relevance of our findings for eukaryotic Elp3s and should aid in understanding the cellular functions and pathophysiological roles of Elongator. << Less

Nat. Struct. Mol. Biol. 23:794-802(2016) [PubMed] [EuropePMC]
Archaeal Elp3 catalyzes tRNA wobble uridine modification at C5 via a radical mechanism.

Selvadurai K., Wang P., Seimetz J., Huang R.H.

Approximately 25% of cytoplasmic tRNAs in eukaryotic organisms have the wobble uridine (U34) modified at C5 through a process that, according to genetic studies, is carried out by the eukaryotic Elongator complex. Here we show that a single archaeal protein, the homolog of the third subunit of the ... >> More

Approximately 25% of cytoplasmic tRNAs in eukaryotic organisms have the wobble uridine (U34) modified at C5 through a process that, according to genetic studies, is carried out by the eukaryotic Elongator complex. Here we show that a single archaeal protein, the homolog of the third subunit of the eukaryotic Elongator complex (Elp3), is able to catalyze the same reaction. The mechanism of action by Elp3 described here represents unprecedented chemistry performed on acetyl-CoA. << Less

Nat. Chem. Biol. 10:810-812(2014) [PubMed] [EuropePMC]

RHEA:61023 acetyl-CoA + H2O + S-adenosyl-L-methionine + uridine(34) in tRNA <=> 5'-deoxyadenosine + 5-(carboxymethyl)uridine(34) in tRNA + CoA + 2 H(+) + L-methionine Reaction with equal flow from both directions. help_outline

Reaction participants Show >> << Hide

Cross-references

Publications

The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase.

Structural basis for tRNA modification by Elp3 from Dehalococcoides mccartyi.

Archaeal Elp3 catalyzes tRNA wobble uridine modification at C5 via a radical mechanism.

RHEA:61023 acetyl-CoA + H2O + S-adenosyl-L-methionine + uridine(34) in tRNA <=> 5'-deoxyadenosine + 5-(carboxymethyl)uridine(34) in tRNA + CoA + 2 H(+) + L-methionine Reaction with equal flow from both directions. ^help_outline