1k6e: Difference between revisions

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Revision as of 13:13, 20 March 2008

File:1k6e.gif

, resolution 1.85Å

Ligands:

, , , and

Activity:

Haloalkane dehalogenase, with EC number 3.8.1.5

Coordinates:

save as pdb, mmCIF, xml

COMPLEX OF HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROM SPHINGOMONAS PAUCIMOBILIS UT26 WITH 1,2-PROPANEDIOL (PRODUCT OF DEHALOGENATION OF 1,2-DIBROMOPROPANE) AT 1.85A

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

1K6E is a Single protein structure of sequence from Sphingomonas paucimobilis. 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

Page seeded by OCA on Thu Mar 20 12:13:09 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1k6e.gif|left|200px]]<br /><applet load="1k6e" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:1k6e.gif|left|200px]]
-caption="1k6e, resolution 1.85&Aring;" />
-'''COMPLEX OF HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROM SPHINGOMONAS PAUCIMOBILIS UT26 WITH 1,2-PROPANEDIOL (PRODUCT OF DEHALOGENATION OF 1,2-DIBROMOPROPANE) AT 1.85A'''<br />
+ {{Structure
+|PDB= 1k6e |SIZE=350|CAPTION= <scene name='initialview01'>1k6e</scene>, resolution 1.85&Aring;
+|SITE=
+|LIGAND= <scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PGO:1,2-PROPANEDIOL'>PGO</scene> and <scene name='pdbligand=1BP:1-BROMOPROPANE-2-OL'>1BP</scene>
+|ACTIVITY= [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]
+|GENE=
+}}
+'''COMPLEX OF HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROM SPHINGOMONAS PAUCIMOBILIS UT26 WITH 1,2-PROPANEDIOL (PRODUCT OF DEHALOGENATION OF 1,2-DIBROMOPROPANE) AT 1.85A'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-K6E 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>, <scene name='pdbligand=PGO:'>PGO</scene> and <scene name='pdbligand=1BP:'>1BP</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=1K6E OCA].
+K6E is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K6E OCA].
 ==Reference==
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12939138 12939138]
+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:[http://www.ncbi.nlm.nih.gov/pubmed/12939138 12939138]
 [[Category: Haloalkane dehalogenase]]
 [[Category: Single protein]]
@@ Line 30: / Line 39: @@
 [[Category: lindane]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:30:37 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:13:09 2008''