1mdr: Difference between revisions

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 <StructureSection load='1mdr' size='340' side='right'caption='[[1mdr]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1mdr]] is a 1 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=1MDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MDR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1mdr]] is a 1 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=1MDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MDR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=APG:ATROLACTIC+ACID+(2-PHENYL-LACTIC+ACID)'>APG</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]] 2.1&#8491;</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>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APG:ATROLACTIC+ACID+(2-PHENYL-LACTIC+ACID)'>APG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=1mdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mdr OCA], [http://pdbe.org/1mdr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mdr RCSB], [http://www.ebi.ac.uk/pdbsum/1mdr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1mdr 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=1mdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mdr OCA], [https://pdbe.org/1mdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mdr RCSB], [https://www.ebi.ac.uk/pdbsum/1mdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mdr ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/MANR_PSEPU MANR_PSEPU]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1mdr ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The mechanism of irreversible inactivation of mandelate racemase (MR) from Pseudomonas putida by alpha-phenylglycidate (alpha PGA) has been investigated stereochemically and crystallographically. The (R) and (S) enantiomers of alpha PGA were synthesized in high enantiomeric excess (81% ee and 83% ee, respectively) using Sharpless epoxidation chemistry. (R)-alpha PGA was determined to be a stereospecific and stoichiometric irreversible inactivator of MR. (S)-alpha PGA does not inactivate MR and appears to bind noncovalently to the active site of MR with less affinity than that of (R)-alpha PGA. The X-ray crystal structure (2.0-A resolution) of MR inactivated by (R)-alpha PGA revealed the presence of a covalent adduct formed by nucleophilic attack of the epsilon-amino group of Lys 166 on the distal carbon on the epoxide ring of (R)-alpha PGA. The proximity of the alpha-proton of (S)-mandelate to Lys 166 [configurationally equivalent to (R)-alpha PGA] was corroborated by the crystal structure (2.1-A resolution) of MR complexed with the substrate analog/competitive inhibitor, (S)-atrolactate [(S)-alpha-methylmandelate]. These results support the proposal that Lys 166 is the polyvalent acid/base responsible for proton transfers on the (S) face of mandelate. In addition, the high-resolution structures also provide insight into the probable interactions of mandelate with the essential Mg2+ and functional groups in the active site.
-The role of lysine 166 in the mechanism of mandelate racemase from Pseudomonas putida: mechanistic and crystallographic evidence for stereospecific alkylation by (R)-alpha-phenylglycidate.,Landro JA, Gerlt JA, Kozarich JW, Koo CW, Shah VJ, Kenyon GL, Neidhart DJ, Fujita S, Petsko GA Biochemistry. 1994 Jan 25;33(3):635-43. PMID:8292591<ref>PMID:8292591</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1mdr" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Mandelate racemase|Mandelate racemase]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus fluorescens putidus flugge 1886]]
 [[Category: Large Structures]]
-[[Category: Mandelate racemase]]
+[[Category: Pseudomonas putida]]
-[[Category: Fujita, S]]
+[[Category: Fujita S]]
-[[Category: Gerlt, J A]]
+[[Category: Gerlt JA]]
-[[Category: Kenyon, G L]]
+[[Category: Kenyon GL]]
-[[Category: Koo, C W]]
+[[Category: Koo CW]]
-[[Category: Kozarich, J W]]
+[[Category: Kozarich JW]]
-[[Category: Landro, J A]]
+[[Category: Landro JA]]
-[[Category: Neidhart, D J]]
+[[Category: Neidhart DJ]]
-[[Category: Petsko, G A]]
+[[Category: Petsko GA]]
-[[Category: Shah, V J]]
+[[Category: Shah VJ]]
-[[Category: Racemase]]