1d07: Difference between revisions

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Revision as of 11:31, 20 March 2008

File:1d07.jpg

, resolution 2.00Å

Ligands:

and

Activity:

Haloalkane dehalogenase, with EC number 3.8.1.5

Coordinates:

save as pdb, mmCIF, xml

HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROM SPHINGOMONAS PAUCIMOBILIS UT26 WITH 1,3-PROPANEDIOL, A PRODUCT OF DEBROMIDATION OF DIBROMPROPANE, AT 2.0A RESOLUTION

OverviewOverview

The haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) is the enzyme involved in the degradation of the important environmental pollutant gamma-hexachlorocyclohexane. The enzyme hydrolyzes a broad range of halogenated cyclic and aliphatic compounds. Here, we present the 1.58 A crystal structure of LinB and the 2.0 A structure of LinB with 1,3-propanediol, a product of debromination of 1,3-dibromopropane, in the active site of the enzyme. The enzyme belongs to the alpha/beta hydrolase family and contains a catalytic triad (Asp108, His272, and Glu132) in the lipase-like topological arrangement previously proposed from mutagenesis experiments. The LinB structure was compared with the structures of haloalkane dehalogenase from Xanthobacter autotrophicus GJ10 and from Rhodococcus sp. and the structural features involved in the adaptation toward xenobiotic substrates were identified. The arrangement and composition of the alpha-helices in the cap domain results in the differences in the size and shape of the active-site cavity and the entrance tunnel. This is the major determinant of the substrate specificity of this haloalkane dehalogenase.

About this StructureAbout this Structure

1D07 is a Single protein structure of sequence from Sphingomonas paucimobilis. Full crystallographic information is available from OCA.

ReferenceReference

Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26., Marek J, Vevodova J, Smatanova IK, Nagata Y, Svensson LA, Newman J, Takagi M, Damborsky J, Biochemistry. 2000 Nov 21;39(46):14082-6. PMID:11087355

Page seeded by OCA on Thu Mar 20 10:31:10 2008

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OCA

@@ Line 1: / Line 1: @@
-[[Image:1d07.jpg|left|200px]]<br /><applet load="1d07" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:1d07.jpg|left|200px]]
-caption="1d07, resolution 2.00&Aring;" />
-'''HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROM SPHINGOMONAS PAUCIMOBILIS UT26 WITH 1,3-PROPANEDIOL, A PRODUCT OF DEBROMIDATION OF DIBROMPROPANE, AT 2.0A RESOLUTION'''<br />
+ {{Structure
+|PDB= 1d07 |SIZE=350|CAPTION= <scene name='initialview01'>1d07</scene>, resolution 2.00&Aring;
+|SITE=
+|LIGAND= <scene name='pdbligand=BR:BROMIDE+ION'>BR</scene> and <scene name='pdbligand=PDO:1,3-PROPANDIOL'>PDO</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=
+}}
+'''HYDROLYTIC HALOALKANE DEHALOGENASE LINB FROM SPHINGOMONAS PAUCIMOBILIS UT26 WITH 1,3-PROPANEDIOL, A PRODUCT OF DEBROMIDATION OF DIBROMPROPANE, AT 2.0A RESOLUTION'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-D07 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> and <scene name='pdbligand=PDO:'>PDO</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=1D07 OCA].
+D07 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=1D07 OCA].
 ==Reference==
-Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26., Marek J, Vevodova J, Smatanova IK, Nagata Y, Svensson LA, Newman J, Takagi M, Damborsky J, Biochemistry. 2000 Nov 21;39(46):14082-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11087355 11087355]
+Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26., Marek J, Vevodova J, Smatanova IK, Nagata Y, Svensson LA, Newman J, Takagi M, Damborsky J, Biochemistry. 2000 Nov 21;39(46):14082-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11087355 11087355]
 [[Category: Haloalkane dehalogenase]]
 [[Category: Single protein]]
@@ Line 29: / Line 38: @@
 [[Category: lindane]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:11:31 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:31:10 2008''