1mdr: Difference between revisions

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New page: left|200px<br /><applet load="1mdr" size="450" color="white" frame="true" align="right" spinBox="true" caption="1mdr, resolution 2.1Å" /> '''THE ROLE OF LYSINE 16...
 
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[[Image:1mdr.gif|left|200px]]<br /><applet load="1mdr" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1mdr, resolution 2.1&Aring;" />
'''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'''<br />


==Overview==
==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==
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.
<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 [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='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='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'>[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]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/md/1mdr_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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>


==About this Structure==
==See Also==
1MDR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida] with MG and APG as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1MDR OCA].
*[[Mandelate racemase|Mandelate racemase]]
 
__TOC__
==Reference==
</StructureSection>
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8292591 8292591]
[[Category: Large Structures]]
[[Category: Mandelate racemase]]
[[Category: Pseudomonas putida]]
[[Category: Pseudomonas putida]]
[[Category: Single protein]]
[[Category: Fujita S]]
[[Category: Fujita, S.]]
[[Category: Gerlt JA]]
[[Category: Gerlt, J.A.]]
[[Category: Kenyon GL]]
[[Category: Kenyon, G.L.]]
[[Category: Koo CW]]
[[Category: Koo, C.W.]]
[[Category: Kozarich JW]]
[[Category: Kozarich, J.W.]]
[[Category: Landro JA]]
[[Category: Landro, J.A.]]
[[Category: Neidhart DJ]]
[[Category: Neidhart, D.J.]]
[[Category: Petsko GA]]
[[Category: Petsko, G.A.]]
[[Category: Shah VJ]]
[[Category: Shah, V.J.]]
[[Category: APG]]
[[Category: MG]]
[[Category: racemase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:21:04 2007''

Latest revision as of 10:43, 14 February 2024

THE ROLE OF LYSINE 166 IN THE MECHANISM OF MANDELATE RACEMASE FROM PSEUDOMONAS PUTIDA: MECHANISTIC AND CRYSTALLOGRAPHIC EVIDENCE FOR STEREOSPECIFIC ALKYLATION BY (R)-ALPHA-PHENYLGLYCIDATETHE ROLE OF LYSINE 166 IN THE MECHANISM OF MANDELATE RACEMASE FROM PSEUDOMONAS PUTIDA: MECHANISTIC AND CRYSTALLOGRAPHIC EVIDENCE FOR STEREOSPECIFIC ALKYLATION BY (R)-ALPHA-PHENYLGLYCIDATE

Structural highlights

1mdr is a 1 chain structure with sequence from Pseudomonas putida. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MANR_PSEPU

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1mdr, resolution 2.10Å

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