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| | <StructureSection load='6q70' size='340' side='right'caption='[[6q70]], [[Resolution|resolution]] 2.05Å' scene=''> | | <StructureSection load='6q70' size='340' side='right'caption='[[6q70]], [[Resolution|resolution]] 2.05Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6q70]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q70 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6Q70 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6q70]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Q70 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Q70 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 2.05Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5irp|5irp]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">alr2, yncD, BSU17640 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=6q70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q70 OCA], [https://pdbe.org/6q70 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6q70 RCSB], [https://www.ebi.ac.uk/pdbsum/6q70 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6q70 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/Alanine_racemase Alanine racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.1 5.1.1.1] </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=6q70 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6q70 OCA], [http://pdbe.org/6q70 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6q70 RCSB], [http://www.ebi.ac.uk/pdbsum/6q70 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6q70 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ALR2_BACSU ALR2_BACSU]] Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids. | + | [https://www.uniprot.org/uniprot/ALR2_BACSU ALR2_BACSU] Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6q70" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6q70" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Alanine racemase 3D structures|Alanine racemase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Vibrio subtilis ehrenberg 1835]] | + | [[Category: Bacillus subtilis]] |
| - | [[Category: Alanine racemase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bernardo-Garcia, N]] | + | [[Category: Bernardo-Garcia N]] |
| - | [[Category: Gago, F]] | + | [[Category: Gago F]] |
| - | [[Category: Hermoso, J A]] | + | [[Category: Hermoso JA]] |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Molecular modeling]]
| + | |
| - | [[Category: Racemase]]
| + | |
| Structural highlights
Function
ALR2_BACSU Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids.
Publication Abstract from PubMed
Pyridoxal 5'-phosphate (PLP) is a versatile cofactor involved in a large variety of enzymatic processes. Most of PLP-catalysed reactions, such as those of alanine racemases (AlaRs), present a common resting state in which the PLP is covalently bound to an active-site lysine to form an internal aldimine. The crystal structure of BsAlaR grown in the presence of Tris lacks this covalent linkage and the PLP cofactor appears deformylated. However, loss of activity in a Tris buffer only occurred after the solution was frozen prior to carrying out the enzymatic assay. This evidence strongly suggests that Tris can access the active site at subzero temperatures and behave as an alternate racemase substrate leading to mechanism-based enzyme inactivation, a hypothesis that is supported by additional X-ray structures and theoretical results from QM/MM calculations. Taken together, our findings highlight a possibly underappreciated role for a common buffer component widely used in biochemical and biophysical experiments.
Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase.,Bernardo-Garcia N, Sanchez-Murcia PA, Espaillat A, Martinez-Caballero S, Cava F, Hermoso JA, Gago F Org Biomol Chem. 2019 Apr 12. doi: 10.1039/c9ob00223e. PMID:30977502[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Bernardo-Garcia N, Sanchez-Murcia PA, Espaillat A, Martinez-Caballero S, Cava F, Hermoso JA, Gago F. Cold-induced aldimine bond cleavage by Tris in Bacillus subtilis alanine racemase. Org Biomol Chem. 2019 Apr 12. doi: 10.1039/c9ob00223e. PMID:30977502 doi:http://dx.doi.org/10.1039/c9ob00223e
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