2pky | pdb_00002pky

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

spinqualitylabelsall models 2pky, resolution 1.55Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2pky is a 1 chain structure with sequence from "corynebacterium_autotrophicum"_baumgarten_et_al._1974 "corynebacterium autotrophicum" baumgarten et al. 1974. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Gene: dhlA ("Corynebacterium autotrophicum" Baumgarten et al. 1974) Activity: Haloalkane dehalogenase, with EC number 3.8.1.5 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum 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. Publication Abstract from PubMed 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. 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Dehalogenase

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