3vot

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Current revision (08:41, 20 March 2024) (edit) (undo)
 
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<StructureSection load='3vot' size='340' side='right'caption='[[3vot]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='3vot' size='340' side='right'caption='[[3vot]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3vot]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacld Bacld]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VOT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VOT FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3vot]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_licheniformis_DSM_13_=_ATCC_14580 Bacillus licheniformis DSM 13 = ATCC 14580]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VOT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VOT FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BL00235, BLi04240 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=279010 BACLD])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/L-amino-acid_alpha-ligase L-amino-acid alpha-ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.28 6.3.2.28] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vot OCA], [https://pdbe.org/3vot PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vot RCSB], [https://www.ebi.ac.uk/pdbsum/3vot PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vot ProSAT]</span></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=3vot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vot OCA], [https://pdbe.org/3vot PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vot RCSB], [https://www.ebi.ac.uk/pdbsum/3vot PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vot ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q65D11_BACLD Q65D11_BACLD]
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L-Amino-acid ligases (LALs) are enzymes which catalyze the formation of dipeptides by linking two L-amino acids. Although many dipeptides are known and expected to have medical and nutritional benefits, their practical use has been limited owing to their low availability and high expense. LALs are potentially desirable tools for the efficient production of dipeptides; however, the molecular basis of substrate recognition by LAL has not yet been sufficiently elucidated for the design of ideal LALs for the desired dipeptides. This report presents the crystal structure of the LAL BL00235 derived from Bacillus licheniformis NBRC 12200 determined at 1.9 A resolution using the multi-wavelength anomalous dispersion method. The overall structure of BL00235 is fairly similar to that of YwfE, the only LAL with a known structure, but the structure around the catalytic site contains some significant differences. Detailed structural comparison of BL00235 with YwfE sheds some light on the molecular basis of the substrate specificities.
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The structure of L-amino-acid ligase from Bacillus licheniformis.,Suzuki M, Takahashi Y, Noguchi A, Arai T, Yagasaki M, Kino K, Saito JI Acta Crystallogr D Biol Crystallogr. 2012 Nov;68(Pt 11):1535-40. doi:, 10.1107/S0907444912038103. Epub 2012 Oct 13. PMID:23090402<ref>PMID:23090402</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3vot" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacld]]
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[[Category: Bacillus licheniformis DSM 13 = ATCC 14580]]
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[[Category: L-amino-acid alpha-ligase]]
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[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Arai, T]]
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[[Category: Arai T]]
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[[Category: Kino, K]]
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[[Category: Kino K]]
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[[Category: Noguchi, A]]
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[[Category: Noguchi A]]
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[[Category: Saito, J]]
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[[Category: Saito J]]
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[[Category: Suzuki, M]]
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[[Category: Suzuki M]]
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[[Category: Takahashi, Y]]
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[[Category: Takahashi Y]]
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[[Category: Yagasaki, M]]
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[[Category: Yagasaki M]]
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[[Category: Atp-binding]]
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[[Category: Atp-grasp motif]]
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[[Category: Ligase]]
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Current revision

Crystal structure of L-amino acid ligase from Bacillus licheniformis

PDB ID 3vot

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