5irp: Difference between revisions
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<StructureSection load='5irp' size='340' side='right'caption='[[5irp]], [[Resolution|resolution]] 2.10Å' scene=''> | <StructureSection load='5irp' size='340' side='right'caption='[[5irp]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5irp]] is a 2 chain structure with sequence from [ | <table><tr><td colspan='2'>[[5irp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IRP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IRP 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=CO2:CARBON+DIOXIDE'>CO2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=UAH:(5-HYDROXY-6-METHYLPYRIDIN-3-YL)METHYL+DIHYDROGEN+PHOSPHATE'>UAH</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</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=CO2:CARBON+DIOXIDE'>CO2</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=UAH:(5-HYDROXY-6-METHYLPYRIDIN-3-YL)METHYL+DIHYDROGEN+PHOSPHATE'>UAH</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=5irp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5irp OCA], [https://pdbe.org/5irp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5irp RCSB], [https://www.ebi.ac.uk/pdbsum/5irp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5irp ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [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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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Bacillus subtilis subsp. subtilis str. 168]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Bernardo-Garcia | [[Category: Bernardo-Garcia N]] | ||
[[Category: Gago | [[Category: Gago F]] | ||
[[Category: Hermoso | [[Category: Hermoso JA]] | ||
Latest revision as of 17:07, 30 August 2023
Crystal structure of the alanine racemase Bsu17640 from Bacillus subtilisCrystal structure of the alanine racemase Bsu17640 from Bacillus subtilis
Structural highlights
FunctionALR2_BACSU Catalyzes the interconversion of L-alanine and D-alanine. May also act on other amino acids. Publication Abstract from PubMedPyridoxal 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 AlsoReferences
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