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2yxp

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(New page: 200px<br /><applet load="2yxp" size="450" color="white" frame="true" align="right" spinBox="true" caption="2yxp, resolution 1.53&Aring;" /> '''The Effect of Deuter...)
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[[Image:2yxp.jpg|left|200px]]<br /><applet load="2yxp" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2yxp, resolution 1.53&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='2yxp' size='340' side='right'caption='[[2yxp]], [[Resolution|resolution]] 1.53&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2yxp]] 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=2YXP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YXP 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]] 1.53&#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=2yxp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yxp OCA], [https://pdbe.org/2yxp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yxp RCSB], [https://www.ebi.ac.uk/pdbsum/2yxp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yxp 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/yx/2yxp_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=2yxp ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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2YXP 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=2YXP OCA].
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*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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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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[[Category: Large Structures]]
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[[Category: Haloalkane dehalogenase]]
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[[Category: Single protein]]
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[[Category: Xanthobacter autotrophicus]]
[[Category: Xanthobacter autotrophicus]]
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[[Category: Hanson, L.]]
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[[Category: Hanson L]]
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[[Category: Langan, P.]]
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[[Category: Langan P]]
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[[Category: Liu, X.]]
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[[Category: Liu X]]
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[[Category: Viola, R.E.]]
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[[Category: Viola RE]]
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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 Tue Nov 20 19:34:41 2007''
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Current revision

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

PDB ID 2yxp

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