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[[Image:2yxp.jpg|left|200px]]


{{Structure
==The Effect of Deuteration on Protein Structure A High Resolution Comparison of Hydrogenous and Perdeuterated Haloalkane Dehalogenase==
|PDB= 2yxp |SIZE=350|CAPTION= <scene name='initialview01'>2yxp</scene>, resolution 1.53&Aring;
<StructureSection load='2yxp' size='340' side='right'caption='[[2yxp]], [[Resolution|resolution]] 1.53&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND=  
<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>
|ACTIVITY= <span class='plainlinks'>[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] </span>
</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>
|GENE= dhlA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=280 Xanthobacter autotrophicus])
<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>
|DOMAIN=
</table>
|RELATEDENTRY=[[2pky|2PKY]]
== Function ==
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2yxp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yxp OCA], [http://www.ebi.ac.uk/pdbsum/2yxp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2yxp RCSB]</span>
[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.
}}
== 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/yx/2yxp_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=2yxp ConSurf].
<div style="clear:both"></div>


'''The Effect of Deuteration on Protein Structure A High Resolution Comparison of Hydrogenous and Perdeuterated Haloalkane Dehalogenase'''
==See Also==
 
*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
 
__TOC__
==Overview==
</StructureSection>
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.
[[Category: Large Structures]]
 
==About this Structure==
2YXP is a [[Single protein]] structure of sequence from [http://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].
 
==Reference==
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://www.ncbi.nlm.nih.gov/pubmed/17704569 17704569]
[[Category: Haloalkane dehalogenase]]
[[Category: Single protein]]
[[Category: Xanthobacter autotrophicus]]
[[Category: Xanthobacter autotrophicus]]
[[Category: Hanson, L.]]
[[Category: Hanson L]]
[[Category: Langan, P.]]
[[Category: Langan P]]
[[Category: Liu, X.]]
[[Category: Liu X]]
[[Category: Viola, R E.]]
[[Category: Viola RE]]
[[Category: haloalkane dehalogenase]]
[[Category: high resolution structure,catalytic mechanism]]
[[Category: hydrolase]]
[[Category: protein deuteration]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:16:21 2008''

Latest revision as of 12:24, 21 February 2024

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

Structural highlights

2yxp is a 1 chain structure with sequence from Xanthobacter autotrophicus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.53Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.

Evolutionary Conservation

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

See Also

2yxp, resolution 1.53Å

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