2pky

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(New page: 200px<br /><applet load="2pky" size="450" color="white" frame="true" align="right" spinBox="true" caption="2pky, resolution 1.55&Aring;" /> '''The Effect of Deuter...)
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[[Image:2pky.jpg|left|200px]]<br /><applet load="2pky" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2pky, resolution 1.55&Aring;" />
 
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'''The Effect of Deuteration on Protein Structure A High Resolution Comparison of Hydrogenous and Perdeuterated Haloalkane Dehalogenase'''<br />
 
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==Overview==
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==The Effect of Deuteration on Protein Structure A High Resolution Comparison of Hydrogenous and Perdeuterated Haloalkane Dehalogenase==
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Haloalkane dehalogenase from Xanthobacter autotrophicus (XaDHL) was, overexpressed under different isotopic conditions to produce fully, hydrogenous (h-XaDHL) and perdeuterated (d-XaDHL) enzyme forms. Deuterium, atoms at labile positions were allowed to back-exchange during, purification and hydrogenous solutions were used for crystallization., Optimal crystals of h-XaDHL and d-XaDHL were obtained under different pH, conditions (pH 6.0 and 4.6, respectively) but had similar P2(1)2(1)2 unit, cells. X-ray diffraction data were refined to 1.53 A (h-XaDHL) and 1.55 A, (d-XaDHL) with excellent overall statistics. The conformations of h-XaDHL, and d-XaDHL are similar, with slightly altered surface regions because of, different packing environments, and h-XaDHL is found to have a more, hydrophobic core than d-XaDHL. The active site of h-XaDHL is similar to, those of previously determined structures, but the active site of d-XaDHL, unexpectedly has some crucial differences. Asp124, the primary nucleophile, in the hydrolysis of haloalkane substrates, is displaced from its position, in h-XaDHL and rotates to form a hydrogen bond with His289. As a, consequence, the water molecule proposed to function as the nucleophile in, the next catalytic step is excluded from the active site. This is the, first observation of this unusual active-site configuration, which is, obtained as a result of perdeuteration that decreases the hydrophobicity, of the enzyme, therefore shifting the optimal pH of crystallization. This, d-XaDHL structure is likely to represent the termination state of the, catalytic reaction and provides an explanation for the acid inhibition of, XaDHL. These results underline the importance of carefully verifying the, assumption that isotopic substitution does not produce significant, structural changes in protein structures.
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<StructureSection load='2pky' size='340' side='right'caption='[[2pky]], [[Resolution|resolution]] 1.55&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2pky]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthobacter_autotrophicus Xanthobacter autotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PKY FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.55&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pky OCA], [https://pdbe.org/2pky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pky RCSB], [https://www.ebi.ac.uk/pdbsum/2pky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pky ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DHLA_XANAU DHLA_XANAU] Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons. Has a broad substrate specificity, which includes terminally mono- and di- chlorinated and brominated alkanes (up to C4 only). The highest activity was found with 1,2-dichloroethane, 1,3-dichloropropane, and 1,2-dibromoethane.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pk/2pky_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=2pky ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Haloalkane dehalogenase from Xanthobacter autotrophicus (XaDHL) was overexpressed under different isotopic conditions to produce fully hydrogenous (h-XaDHL) and perdeuterated (d-XaDHL) enzyme forms. Deuterium atoms at labile positions were allowed to back-exchange during purification and hydrogenous solutions were used for crystallization. Optimal crystals of h-XaDHL and d-XaDHL were obtained under different pH conditions (pH 6.0 and 4.6, respectively) but had similar P2(1)2(1)2 unit cells. X-ray diffraction data were refined to 1.53 A (h-XaDHL) and 1.55 A (d-XaDHL) with excellent overall statistics. The conformations of h-XaDHL and d-XaDHL are similar, with slightly altered surface regions because of different packing environments, and h-XaDHL is found to have a more hydrophobic core than d-XaDHL. The active site of h-XaDHL is similar to those of previously determined structures, but the active site of d-XaDHL unexpectedly has some crucial differences. Asp124, the primary nucleophile in the hydrolysis of haloalkane substrates, is displaced from its position in h-XaDHL and rotates to form a hydrogen bond with His289. As a consequence, the water molecule proposed to function as the nucleophile in the next catalytic step is excluded from the active site. This is the first observation of this unusual active-site configuration, which is obtained as a result of perdeuteration that decreases the hydrophobicity of the enzyme, therefore shifting the optimal pH of crystallization. This d-XaDHL structure is likely to represent the termination state of the catalytic reaction and provides an explanation for the acid inhibition of XaDHL. These results underline the importance of carefully verifying the assumption that isotopic substitution does not produce significant structural changes in protein structures.
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==About this Structure==
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The effect of deuteration on protein structure: a high-resolution comparison of hydrogenous and perdeuterated haloalkane dehalogenase.,Liu X, Hanson BL, Langan P, Viola RE Acta Crystallogr D Biol Crystallogr. 2007 Sep;63(Pt 9):1000-8. Epub 2007, Aug 17. PMID:17704569<ref>PMID:17704569</ref>
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2PKY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Xanthobacter_autotrophicus Xanthobacter autotrophicus]. Active as [http://en.wikipedia.org/wiki/Haloalkane_dehalogenase Haloalkane dehalogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.5 3.8.1.5] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2PKY OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The effect of deuteration on protein structure: a high-resolution comparison of hydrogenous and perdeuterated haloalkane dehalogenase., Liu X, Hanson BL, Langan P, Viola RE, Acta Crystallogr D Biol Crystallogr. 2007 Sep;63(Pt 9):1000-8. Epub 2007, Aug 17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17704569 17704569]
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</div>
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[[Category: Haloalkane dehalogenase]]
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<div class="pdbe-citations 2pky" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Xanthobacter autotrophicus]]
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[[Category: Hanson, L.]]
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[[Category: Langan, P.]]
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[[Category: Liu, X.]]
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[[Category: Viola, R.E.]]
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[[Category: catalytic mechanism]]
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[[Category: haloalkane dehalogenase]]
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[[Category: high resolution structure]]
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[[Category: hydrolase]]
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[[Category: protein deuteration]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:34:41 2007''
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==See Also==
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*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Xanthobacter autotrophicus]]
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[[Category: Hanson L]]
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[[Category: Langan P]]
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[[Category: Liu X]]
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[[Category: Viola RE]]

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The Effect of Deuteration on Protein Structure A High Resolution Comparison of Hydrogenous and Perdeuterated Haloalkane Dehalogenase

PDB ID 2pky

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