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| | ==P. putida mandelate racemase co-crystallized with 3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl) propionic acid== | | ==P. putida mandelate racemase co-crystallized with 3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl) propionic acid== |
| - | <StructureSection load='4fp1' size='340' side='right' caption='[[4fp1]], [[Resolution|resolution]] 1.68Å' scene=''> | + | <StructureSection load='4fp1' size='340' side='right'caption='[[4fp1]], [[Resolution|resolution]] 1.68Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4fp1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_fluorescens_putidus"_flugge_1886 "bacillus fluorescens putidus" flugge 1886]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FP1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FP1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4fp1]] is a 2 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=4FP1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FP1 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BFM:3,3,3-TRIFLUORO-2-HYDROXY-2-(TRIFLUOROMETHYL)PROPANOIC+ACID'>BFM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.68Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3uxk|3uxk]], [[3uxl|3uxl]], [[4fp0|4fp0]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BFM:3,3,3-TRIFLUORO-2-HYDROXY-2-(TRIFLUOROMETHYL)PROPANOIC+ACID'>BFM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mdlA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 "Bacillus fluorescens putidus" Flugge 1886])</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=4fp1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fp1 OCA], [https://pdbe.org/4fp1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fp1 RCSB], [https://www.ebi.ac.uk/pdbsum/4fp1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fp1 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/Mandelate_racemase Mandelate racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.2.2 5.1.2.2] </span></td></tr>
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| - | <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=4fp1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fp1 OCA], [http://pdbe.org/4fp1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fp1 RCSB], [http://www.ebi.ac.uk/pdbsum/4fp1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fp1 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/MANR_PSEPU MANR_PSEPU] |
| - | Mandelate racemase (MR) from Pseudomonas putida catalyzes the Mg(2+)-dependent 1,1-proton transfer that interconverts the enantiomers of mandelate. Because trifluorolactate is also a substrate of MR, we anticipated that replacing the phenyl rings of the competitive, substrate-product analogue inhibitor benzilate (Ki = 0.7 mM) with trifluoromethyl groups might furnish an inhibitor. Surprisingly, the substrate-product analogue 3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl)propanoate (TFHTP) was a potent competitive inhibitor [Ki = 27 +/- 4 muM; cf. Km = 1.2 mM for both (R)-mandelate and (R)-trifluorolactate]. To understand the origins of this high binding affinity, we determined the X-ray crystal structure of the MR-TFHTP complex to 1.68 A resolution. Rather than chelating the active site Mg(2+) with its glycolate moiety, like other ground state analogues, TFHTP exhibited a novel binding mode with the two trifluoromethyl groups closely packed against the 20s loop and the carboxylate bridging the two active site Bronsted acid-base catalysts Lys 166 and His 297. Recognizing that positioning a carboxylate between the Bronsted acid-base catalysts could yield an inhibitor, we showed that tartronate was a competitive inhibitor of MR (Ki = 1.8 +/- 0.1 mM). The X-ray crystal structure of the MR-tartronate complex (1.80 A resolution) revealed that the glycolate moiety of tartronate chelated the Mg(2+) and that the carboxylate bridged Lys 166 and His 297. Models of tartronate in monomers A and B of the crystal structure mimicked the binding orientations of (S)-mandelate and that anticipated for (R)-mandelate, respectively. For the latter monomer, the 20s loop appeared to be disordered, as it also did in the X-ray structure of the MR triple mutant (C92S/C264S/K166C) complexed with benzilate, which was determined to 1.89 A resolution. These observations indicate that the 20s loop likely undergoes a significant conformational change upon binding (R)-mandelate. In general, our observations suggest that inhibitors of other enolase superfamily enzymes may be designed to capitalize on the recognition of the active site Bronsted acid-base catalysts as binding determinants.
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| - | Potent inhibition of mandelate racemase by a fluorinated substrate-product analogue with a novel binding mode.,Nagar M, Lietzan AD, St Maurice M, Bearne SL Biochemistry. 2014 Feb 25;53(7):1169-78. doi: 10.1021/bi401703h. Epub 2014 Feb, 10. PMID:24472022<ref>PMID:24472022</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 4fp1" style="background-color:#fffaf0;"></div>
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| | ==See Also== | | ==See Also== |
| | *[[Mandelate racemase|Mandelate racemase]] | | *[[Mandelate racemase|Mandelate racemase]] |
| - | == References == | |
| - | <references/> | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus fluorescens putidus flugge 1886]] | + | [[Category: Large Structures]] |
| - | [[Category: Mandelate racemase]] | + | [[Category: Pseudomonas putida]] |
| - | [[Category: Lietzan, A D]] | + | [[Category: Lietzan AD]] |
| - | [[Category: St Maurice, M]] | + | [[Category: StMaurice M]] |
| - | [[Category: Enolase superfamily enzyme]]
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| - | [[Category: Isomerase-isomerase inhibitor complex]]
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