1k63: Difference between revisions

Revision as of 14:30, 21 February 2008

Complex of hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis with UT26 2-BROMO-2-PROPENE-1-OL at 1.8A resolution

OverviewOverview

The haloalkane dehalogenases are detoxifying enzymes that convert a broad range of halogenated substrates to the corresponding alcohols. Complete crystal structures of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB), and complexes of LinB with 1,2-propanediol/1-bromopropane-2-ol and 2-bromo-2-propene-1-ol, products of debromination of 1,2-dibromopropane and 2,3-dibromopropene, respectively, were determined from 1.8 A resolution X-ray diffraction data. Published structures of native LinB and its complex with 1,3-propanediol [Marek et al. (2000) Biochemistry 39, 14082-14086] were reexamined. The full and partial debromination of 1,2-dibromopropane and 2,3-dibromopropene, respectively, conformed to the observed general trend that the sp(3)-hybridized carbon is the predominant electrophilic site for the S(N)2 bimolecular nucleophilic substitution in dehalogenation reaction. The 2-bromo-2-propene-1-ol product of 2,3-dibromopropene dehalogenation in crystal was positively identified by the gas chromatography-mass spectroscopy (GC-MS) technique. The 1,2-propanediol and 1-bromopropane-2-ol products of 1,2-dibromopropane dehalogenation in crystal were also supported by the GC-MS identification. Comparison of native LinB with its complexes showed high flexibility of residues 136-157, in particular, Asp146 and Glu147, from the cap domain helices alpha(4) and alpha(5)('). Those residues were shifted mainly in direction toward the ligand molecules in the complex structures. It seems the cap domain moves nearer to the core squeezing substrate into the active center closer to the catalytic triad. This also leads to slight contraction of the whole complex structures. The flexibility detected by crystallographic analysis is in remarkable agreement with flexibility observed by molecular dynamic simulations.

About this StructureAbout this Structure

1K63 is a Single protein structure of sequence from Sphingomonas paucimobilis with , , and as ligands. Active as Haloalkane dehalogenase, with EC number 3.8.1.5 Full crystallographic information is available from OCA.

ReferenceReference

Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates., Streltsov VA, Prokop Z, Damborsky J, Nagata Y, Oakley A, Wilce MC, Biochemistry. 2003 Sep 2;42(34):10104-12. PMID:12939138

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-[[Image:1k63.gif|left|200px]]<br /><applet load="1k63" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1k63.gif|left|200px]]<br /><applet load="1k63" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1k63, resolution 1.80&Aring;" />
 '''Complex of hydrolytic haloalkane dehalogenase linb from sphingomonas paucimobilis with UT26 2-BROMO-2-PROPENE-1-OL at 1.8A resolution'''<br />
 ==Overview==
-The haloalkane dehalogenases are detoxifying enzymes that convert a broad, range of halogenated substrates to the corresponding alcohols. Complete, crystal structures of haloalkane dehalogenase from Sphingomonas, paucimobilis UT26 (LinB), and complexes of LinB with, 1,2-propanediol/1-bromopropane-2-ol and 2-bromo-2-propene-1-ol, products, of debromination of 1,2-dibromopropane and 2,3-dibromopropene, respectively, were determined from 1.8 A resolution X-ray diffraction, data. Published structures of native LinB and its complex with, 1,3-propanediol [Marek et al. (2000) Biochemistry 39, 14082-14086] were, reexamined. The full and partial debromination of 1,2-dibromopropane and, 2,3-dibromopropene, respectively, conformed to the observed general trend, that the sp(3)-hybridized carbon is the predominant electrophilic site for, the S(N)2 bimolecular nucleophilic substitution in dehalogenation, reaction. The 2-bromo-2-propene-1-ol product of 2,3-dibromopropene, dehalogenation in crystal was positively identified by the gas, chromatography-mass spectroscopy (GC-MS) technique. The 1,2-propanediol, and 1-bromopropane-2-ol products of 1,2-dibromopropane dehalogenation in, crystal were also supported by the GC-MS identification. Comparison of, native LinB with its complexes showed high flexibility of residues, 136-157, in particular, Asp146 and Glu147, from the cap domain helices, alpha(4) and alpha(5)('). Those residues were shifted mainly in direction, toward the ligand molecules in the complex structures. It seems the cap, domain moves nearer to the core squeezing substrate into the active center, closer to the catalytic triad. This also leads to slight contraction of, the whole complex structures. The flexibility detected by crystallographic, analysis is in remarkable agreement with flexibility observed by molecular, dynamic simulations.
+The haloalkane dehalogenases are detoxifying enzymes that convert a broad range of halogenated substrates to the corresponding alcohols. Complete crystal structures of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB), and complexes of LinB with 1,2-propanediol/1-bromopropane-2-ol and 2-bromo-2-propene-1-ol, products of debromination of 1,2-dibromopropane and 2,3-dibromopropene, respectively, were determined from 1.8 A resolution X-ray diffraction data. Published structures of native LinB and its complex with 1,3-propanediol [Marek et al. (2000) Biochemistry 39, 14082-14086] were reexamined. The full and partial debromination of 1,2-dibromopropane and 2,3-dibromopropene, respectively, conformed to the observed general trend that the sp(3)-hybridized carbon is the predominant electrophilic site for the S(N)2 bimolecular nucleophilic substitution in dehalogenation reaction. The 2-bromo-2-propene-1-ol product of 2,3-dibromopropene dehalogenation in crystal was positively identified by the gas chromatography-mass spectroscopy (GC-MS) technique. The 1,2-propanediol and 1-bromopropane-2-ol products of 1,2-dibromopropane dehalogenation in crystal were also supported by the GC-MS identification. Comparison of native LinB with its complexes showed high flexibility of residues 136-157, in particular, Asp146 and Glu147, from the cap domain helices alpha(4) and alpha(5)('). Those residues were shifted mainly in direction toward the ligand molecules in the complex structures. It seems the cap domain moves nearer to the core squeezing substrate into the active center closer to the catalytic triad. This also leads to slight contraction of the whole complex structures. The flexibility detected by crystallographic analysis is in remarkable agreement with flexibility observed by molecular dynamic simulations.
 ==About this Structure==
-K63 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis] with BR, CL, MG and BRP as [http://en.wikipedia.org/wiki/ligands ligands]. 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=1K63 OCA].
+K63 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis] with <scene name='pdbligand=BR:'>BR</scene>, <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=BRP:'>BRP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1K63 OCA].
 ==Reference==
@@ Line 15: / Line 15: @@
 [[Category: Sphingomonas paucimobilis]]
 [[Category: Damborsky, J.]]
-[[Category: Streltsov, V.A.]]
+[[Category: Streltsov, V A.]]
-[[Category: Wilce, M.C.J.]]
+[[Category: Wilce, M C.J.]]
 [[Category: BR]]
 [[Category: BRP]]
@@ Line 26: / Line 26: @@
 [[Category: lindane]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 18:53:04 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:30:35 2008''