6spr

From Proteopedia

(Difference between revisions)

Current revision

Structure of the Escherichia coli methionyl-tRNA synthetase variant VI298 complexed with beta-methionine

Structural highlights

6spr is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.48Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SYM_ECOLI Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.[HAMAP-Rule:MF_00098]

Publication Abstract from PubMed

Polypeptides containing beta-amino acids are attractive tools for the design of novel proteins having unique properties of medical or industrial interest. Incorporation of beta-amino acids in vivo requires the development of efficient aminoacyl-tRNA synthetases specific of these non-canonical amino acids. Here, we have performed a detailed structural and biochemical study of the recognition and use of beta(3)-Met by Escherichia coli methionyl-tRNA synthetase (MetRS). We show that MetRS binds beta(3)-Met with a 24-fold lower affinity but catalyzes the esterification of the non-canonical amino acid onto tRNA with a rate lowered by three orders of magnitude. Accurate measurements of the catalytic parameters required careful consideration of the presence of contaminating alpha-Met in beta(3)-Met commercial samples. The 1.45 A crystal structure of the MetRS: beta(3)-Met complex shows that beta(3)-Met binds the enzyme essentially like alpha-Met, but the carboxylate moiety is mobile and not adequately positioned to react with ATP for aminoacyl adenylate formation. This study provides structural and biochemical bases for engineering MetRS with improved beta(3)-Met aminoacylation capabilities.

Use of beta(3)-methionine as an amino acid substrate of Escherichia coli methionyl-tRNA synthetase.,Nigro G, Bourcier S, Lazennec-Schurdevin C, Schmitt E, Marliere P, Mechulam Y J Struct Biol. 2019 Dec 17:107435. doi: 10.1016/j.jsb.2019.107435. PMID:31862305^[1]

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

References

↑ Nigro G, Bourcier S, Lazennec-Schurdevin C, Schmitt E, Marliere P, Mechulam Y. Use of beta(3)-methionine as an amino acid substrate of Escherichia coli methionyl-tRNA synthetase. J Struct Biol. 2019 Dec 17:107435. doi: 10.1016/j.jsb.2019.107435. PMID:31862305 doi:http://dx.doi.org/10.1016/j.jsb.2019.107435

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

Categories: Escherichia coli | Large Structures | Mechulam Y | Nigro G | Schmitt E

@@ Line 3: / Line 3: @@
 <StructureSection load='6spr' size='340' side='right'caption='[[6spr]], [[Resolution|resolution]] 1.48&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6spr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SPR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6SPR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6spr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6SPR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6SPR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B3M:(3R)-3-AMINO-5-(METHYLSULFANYL)PENTANOIC+ACID'>B3M</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.48&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qqt|1qqt]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B3M:(3R)-3-AMINO-5-(METHYLSULFANYL)PENTANOIC+ACID'>B3M</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">metG, b2114, JW2101 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=6spr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6spr OCA], [https://pdbe.org/6spr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6spr RCSB], [https://www.ebi.ac.uk/pdbsum/6spr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6spr ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionine--tRNA_ligase Methionine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.10 6.1.1.10] </span></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=6spr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6spr OCA], [http://pdbe.org/6spr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6spr RCSB], [http://www.ebi.ac.uk/pdbsum/6spr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6spr ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SYM_ECOLI SYM_ECOLI]] Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.[HAMAP-Rule:MF_00098]
+[https://www.uniprot.org/uniprot/SYM_ECOLI SYM_ECOLI] Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation.[HAMAP-Rule:MF_00098]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 19: @@
 </div>
 <div class="pdbe-citations 6spr" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Methionine--tRNA ligase]]
+[[Category: Mechulam Y]]
-[[Category: Mechulam, Y]]
+[[Category: Nigro G]]
-[[Category: Nigro, G]]
+[[Category: Schmitt E]]
-[[Category: Schmitt, E]]
-[[Category: Translation]]
-[[Category: Trna aminoacylation]]

6spr

From Proteopedia

Current revision

Structure of the Escherichia coli methionyl-tRNA synthetase variant VI298 complexed with beta-methionine

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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