7mqx: Difference between revisions

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<StructureSection load='7mqx' size='340' side='right'caption='[[7mqx]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
<StructureSection load='7mqx' size='340' side='right'caption='[[7mqx]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[7mqx]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MQX FirstGlance]. <br>
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MQX FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.914&#8491;</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]] 1.914&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZMD:(3S)-2,1-benzoxaborole-1,3(3H)-diol'>ZMD</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZMD:(3S)-2,1-benzoxaborole-1,3(3H)-diol'>ZMD</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=7mqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mqx OCA], [https://pdbe.org/7mqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mqx RCSB], [https://www.ebi.ac.uk/pdbsum/7mqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mqx 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=7mqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mqx OCA], [https://pdbe.org/7mqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mqx RCSB], [https://www.ebi.ac.uk/pdbsum/7mqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mqx ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/MANR_PSEPU MANR_PSEPU]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
o-Carbonyl arylboronic acids such as 2-formylphenylboronic acid (2-FPBA) are employed in biocompatible conjugation reactions with the resulting iminoboronate adduct stabilized by an intramolecular N-B interaction. However, few studies have utilized these reagents as active site-directed enzyme inhibitors. We show that 2-FPBA is a potent reversible, slow-onset inhibitor of mandelate racemase (MR), an enzyme that has served as a valuable paradigm for understanding enzyme-catalyzed abstraction of an alpha-proton from a carbon acid substrate with a high pKa. Kinetic analysis of the progress curves for the slow onset of inhibition of wild-type MR using a two-step kinetic mechanism gave Ki and Ki* values of 5.1 +/- 1.8 and 0.26 +/- 0.08 muM, respectively. Hence, wild-type MR binds 2-FPBA with an affinity that exceeds that for the substrate by approximately 3000-fold. K164R MR was inhibited by 2-FPBA, while K166R MR was not inhibited, indicating that Lys 166 was essential for inhibition. Unexpectedly, mass spectrometric analysis of the NaCNBH3-treated enzyme-inhibitor complex did not yield evidence of an iminoboronate adduct. (11)B nuclear magnetic resonance spectroscopy of the MR.2-FPBA complex indicated that the boron atom was sp(3)-hybridized (delta 6.0), consistent with dative bond formation. Surprisingly, X-ray crystallography revealed the formation of an N(zeta)-B dative bond between Lys 166 and 2-FPBA with intramolecular cyclization to form a benzoxaborole, rather than the expected iminoboronate. Thus, when o-carbonyl arylboronic acid reagents are employed to modify proteins, the structure of the resulting product depends on the protein architecture at the site of modification.
Slow-Onset, Potent Inhibition of Mandelate Racemase by 2-Formylphenylboronic Acid. An Unexpected Adduct Clasps the Catalytic Machinery.,Douglas CD, Grandinetti L, Easton NM, Kuehm OP, Hayden JA, Hamilton MC, St Maurice M, Bearne SL Biochemistry. 2021 Aug 2. doi: 10.1021/acs.biochem.1c00374. PMID:34339165<ref>PMID:34339165</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7mqx" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Mandelate racemase|Mandelate racemase]]
*[[Mandelate racemase|Mandelate racemase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Pseudomonas putida]]
[[Category: Bearne SL]]
[[Category: Bearne SL]]
[[Category: Grandinetti L]]
[[Category: Grandinetti L]]
[[Category: StMaurice M]]
[[Category: StMaurice M]]

Latest revision as of 11:12, 23 October 2024

P. putida mandelate racemase forms an oxobenzoxaborole adduct with 2-formylphenylboronic acid

7mqx, resolution 1.91Å

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