View source for 1zrm


==CRYSTAL STRUCTURE OF THE REACTION INTERMEDIATE OF L-2-HALOACID DEHALOGENASE WITH 2-CHLORO-N-BUTYRATE==
<StructureSection load='1zrm' size='340' side='right'caption='[[1zrm]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1zrm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._YL Pseudomonas sp. YL]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZRM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZRM 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&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BUA:BUTANOIC+ACID'>BUA</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=1zrm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zrm OCA], [https://pdbe.org/1zrm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zrm RCSB], [https://www.ebi.ac.uk/pdbsum/1zrm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zrm ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/HAD_PSEUY HAD_PSEUY] Catalyzes the hydrolytic dehalogenation of small (S)-2-haloalkanoic acids to yield the corresponding (R)-2-hydroxyalkanoic acids. Acts on acids of short chain lengths, C(2) to C(4), with inversion of configuration at C-2.
== 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/zr/1zrm_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1zrm ConSurf].
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== Publication Abstract from PubMed ==
Crystal structures of L-2-haloacid dehalogenase from Pseudomonas sp. YL complexed with monochloroacetate, L-2-chlorobutyrate, L-2-chloro-3-methylbutyrate, or L-2-chloro-4-methylvalerate were determined at 1.83-, 2.0-, 2.2-, and 2.2-A resolutions, respectively, using the complex crystals prepared with the S175A mutant, which are isomorphous with those of the wild-type enzyme. These structures exhibit unique structural features that correspond to those of the reaction intermediates. In each case, the nucleophile Asp-10 is esterified with the dechlorinated moiety of the substrate. The substrate moieties in all but the monochloroacetate intermediate have a D-configuration at the C2 atom. The overall polypeptide fold of each of the intermediates is similar to that of the wild-type enzyme. However, it is clear that the Asp-10-Ser-20 region moves to the active site in all of the intermediates, and the Tyr-91-Asp-102 and Leu-117-Arg-135 regions make conformational changes in all but the monochloroacetate intermediates. Ser-118 is located near the carboxyl group of the substrate moiety; this residue probably serves as a binding residue for the substrate carboxyl group. The hydrophobic pocket, which is primarily composed of the Tyr-12, Gln-42, Leu-45, Phe-60, Lys-151, Asn-177, and Trp-179 side chains, exists around the alkyl group of the substrate moiety. This pocket may play an important role in stabilizing the alkyl group of the substrate moiety through hydrophobic interactions, and may also play a role in determining the stereospecificity of the enzyme. Moreover, a water molecule, which is absent in the substrate-free enzyme, is present in the vicinities of the carboxyl carbon of Asp-10 and the side chains of Asp-180, Asn-177, and Ala-175 in each intermediate. This water molecule may hydrolyze the ester intermediate and its substrate. These findings crystallographically demonstrate that the enzyme reaction proceeds through the formation of an ester intermediate with the enzyme's nucleophile Asp-10.

Crystal structures of reaction intermediates of L-2-haloacid dehalogenase and implications for the reaction mechanism.,Li YF, Hata Y, Fujii T, Hisano T, Nishihara M, Kurihara T, Esaki N J Biol Chem. 1998 Jun 12;273(24):15035-44. PMID:9614112<ref>PMID:9614112</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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==See Also==
*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pseudomonas sp. YL]]
[[Category: Esaki N]]
[[Category: Fujii T]]
[[Category: Hata Y]]
[[Category: Hisano T]]
[[Category: Kurihara T]]
[[Category: Li Y-F]]
[[Category: Nishihara M]]