6ia6

From Proteopedia

(Difference between revisions)

Current revision

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

Structural highlights

6ia6 is a 1 chain structure with sequence from Dehalococcoides mccartyi BTF08. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.7Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ELP3_DEHMC tRNA uridine(34) acetyltransferase, which mediates formation of carboxymethyluridine in the wobble base at position 34 in tRNAs (PubMed:27455459). 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. Does not show protein lysine acetyltransferase activity (By similarity).[UniProtKB:D5VRB9]^[1]

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^[2]

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

References

↑ Glatt S, Zabel R, Kolaj-Robin O, Onuma OF, Baudin F, Graziadei A, Taverniti V, Lin TY, Baymann F, Seraphin B, Breunig KD, Muller CW. Structural basis for tRNA modification by Elp3 from Dehalococcoides mccartyi. Nat Struct Mol Biol. 2016 Jul 25. doi: 10.1038/nsmb.3265. PMID:27455459 doi:http://dx.doi.org/10.1038/nsmb.3265
↑ 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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6ia6"

Categories: Dehalococcoides mccartyi BTF08 | Large Structures | Glatt S | Lin TY

@@ Line 1: / Line 1: @@
 ==Crystal structure of the bacterial Dehalococcoides mccartyi Elp3 with desulfo-CoA==
-<StructureSection load='6ia6' size='340' side='right' caption='[[6ia6]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='6ia6' size='340' side='right'caption='[[6ia6]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ia6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IA6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IA6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ia6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dehalococcoides_mccartyi_BTF08 Dehalococcoides mccartyi BTF08]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IA6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IA6 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DCA:DESULFO-COENZYME+A'>DCA</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ia6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ia6 OCA], [http://pdbe.org/6ia6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ia6 RCSB], [http://www.ebi.ac.uk/pdbsum/6ia6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ia6 ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DCA:DESULFO-COENZYME+A'>DCA</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6ia6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ia6 OCA], [https://pdbe.org/6ia6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ia6 RCSB], [https://www.ebi.ac.uk/pdbsum/6ia6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ia6 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/ELP3_DEHMC ELP3_DEHMC] tRNA uridine(34) acetyltransferase, which mediates formation of carboxymethyluridine in the wobble base at position 34 in tRNAs (PubMed:27455459). 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. Does not show protein lysine acetyltransferase activity (By similarity).[UniProtKB:D5VRB9]<ref>PMID:27455459</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Glatt, S]]
+[[Category: Dehalococcoides mccartyi BTF08]]
-[[Category: Lin, T Y]]
+[[Category: Large Structures]]
-[[Category: Acetyl-coa hydrolysis]]
+[[Category: Glatt S]]
-[[Category: Elongator complex]]
+[[Category: Lin TY]]
-[[Category: Non-canonical acetyltransferase]]
-[[Category: Transferase]]
-[[Category: Trna binding]]

6ia6

From Proteopedia

Current revision

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

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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