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3r6v

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Current revision (12:12, 14 March 2024) (edit) (undo)
 
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<StructureSection load='3r6v' size='340' side='right'caption='[[3r6v]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
<StructureSection load='3r6v' size='340' side='right'caption='[[3r6v]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3r6v]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._ym55-1 Bacillus sp. ym55-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R6V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R6V FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3r6v]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._YM55-1 Bacillus sp. YM55-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R6V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R6V 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=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.6&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3r6q|3r6q]], [[3r6y|3r6y]]</div></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=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aspB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=96471 Bacillus sp. YM55-1])</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/Aspartate_ammonia-lyase Aspartate ammonia-lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.1 4.3.1.1] </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=3r6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r6v OCA], [https://pdbe.org/3r6v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r6v RCSB], [https://www.ebi.ac.uk/pdbsum/3r6v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r6v 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=3r6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r6v OCA], [https://pdbe.org/3r6v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r6v RCSB], [https://www.ebi.ac.uk/pdbsum/3r6v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r6v 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/Q9LCC6_9BACI Q9LCC6_9BACI]
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Aspartate ammonia lyases (or aspartases) catalyze the reversible deamination of l-aspartate into fumarate and ammonia. The lack of crystal structures of complexes with substrate, product, or substrate analogues so far precluded determination of their precise mechanism of catalysis. Here, we report crystal structures of AspB, the aspartase from Bacillus sp. YM55-1, in an unliganded state and in complex with l-aspartate at 2.4 and 2.6 A resolution, respectively. AspB forces the bound substrate to adopt a high-energy, enediolate-like conformation that is stabilized, in part, by an extensive network of hydrogen bonds between residues Thr101, Ser140, Thr141, and Ser319 and the substrate's beta-carboxylate group. Furthermore, substrate binding induces a large conformational change in the SS loop (residues G(317)SSIMPGKVN(326)) from an open conformation to one that closes over the active site. In the closed conformation, the strictly conserved SS loop residue Ser318 is at a suitable position to act as a catalytic base, abstracting the Cbeta proton of the substrate in the first step of the reaction mechanism. The catalytic importance of Ser318 was confirmed by site-directed mutagenesis. Site-directed mutagenesis of SS loop residues, combined with structural and kinetic analysis of a stable proteolytic AspB fragment, further suggests an important role for the small C-terminal domain of AspB in controlling the conformation of the SS loop and, hence, in regulating catalytic activity. Our results provide evidence supporting the notion that members of the aspartase/fumarase superfamily use a common catalytic mechanism involving general base-catalyzed formation of a stabilized enediolate intermediate.
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Structural basis for the catalytic mechanism of aspartate ammonia lyase.,Fibriansah G, Veetil VP, Poelarends GJ, Thunnissen AM Biochemistry. 2011 Jul 12;50(27):6053-62. Epub 2011 Jun 20. PMID:21661762<ref>PMID:21661762</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 3r6v" 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: Aspartate ammonia-lyase]]
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[[Category: Bacillus sp. YM55-1]]
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[[Category: Bacillus sp. ym55-1]]
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[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Fibriansah, G]]
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[[Category: Fibriansah G]]
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[[Category: Poelarends, G J]]
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[[Category: Poelarends GJ]]
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[[Category: Thunnissen, A M.W H]]
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[[Category: Puthan Veetil V]]
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[[Category: Veetil, V Puthan]]
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[[Category: Thunnissen A-MWH]]
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[[Category: Aspartase]]
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[[Category: Aspartate ammonia lyase]]
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[[Category: Lyase]]
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Current revision

Crystal structure of aspartase from Bacillus sp. YM55-1 with bound L-aspartate

PDB ID 3r6v

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