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1g5f

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Revision as of 07:02, 5 April 2017

STRUCTURE OF LINB COMPLEXED WITH 1,2-DICHLOROETHANE

Structural highlights

1g5f is a 1 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
NonStd Res:
Related:	1g42, 1g4h
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[LINB_SPHPI] 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 since not only monochloroalkanes (C3 to C10) but also dichloroalkanes (> C3), bromoalkanes, and chlorinated aliphatic alcohols were good substrates. Shows almost no activity with 1,2-dichloroethane, but very high activity with the brominated analog. Is involved in the degradation of the important environmental pollutant gamma-hexachlorocyclohexane (lindane) as it also catalyzes conversion of 1,3,4,6-tetrachloro-1,4-cyclohexadiene (1,4-TCDN) to 2,5-dichloro-2,5-cyclohexadiene-1,4-diol (2,5-DDOL) via the intermediate 2,4,5-trichloro-2,5-cyclohexadiene-1-ol (2,4,5-DNOL).

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

The hydrolysis of haloalkanes to their corresponding alcohols and inorganic halides is catalyzed by alpha/beta-hydrolases called haloalkane dehalogenases. The study of haloalkane dehalogenases is vital for the development of these enzymes if they are to be utilized for bioremediation of organohalide-contaminated industrial waste. We report the kinetic and structural analysis of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) in complex with each of 1,2-dichloroethane and 1,2-dichloropropane and the reaction product of 1-chlorobutane turnover. Activity studies showed very weak but detectable activity of LinB with 1,2-dichloroethane [0.012 nmol s(-1) (mg of enzyme)(-1)] and 1,2-dichloropropane [0.027 nmol s(-1) (mg of enzyme)(-1)]. These activities are much weaker compared, for example, to the activity of LinB with 1-chlorobutane [68.2 nmol s(-1) (mg of enzyme)(-1)]. Inhibition analysis reveals that both 1,2-dichloroethane and 1,2-dichloropropane act as simple competitive inhibitors of the substrate 1-chlorobutane and that 1,2-dichloroethane binds to LinB with lower affinity than 1,2-dichloropropane. Docking calculations on the enzyme in the absence of active site water molecules and halide ions confirm that these compounds could bind productively. However, when these moieties were included in the calculations, they bound in a manner similar to that observed in the crystal structure. These data provide an explanation for the low activity of LinB with small, chlorinated alkanes and show the importance of active site water molecules and reaction products in molecular docking.

Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition.,Oakley AJ, Prokop Z, Bohac M, Kmunicek J, Jedlicka T, Monincova M, Kuta-Smatanova I, Nagata Y, Damborsky J, Wilce MC Biochemistry. 2002 Apr 16;41(15):4847-55. PMID:11939779^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Oakley AJ, Prokop Z, Bohac M, Kmunicek J, Jedlicka T, Monincova M, Kuta-Smatanova I, Nagata Y, Damborsky J, Wilce MC. Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition. Biochemistry. 2002 Apr 16;41(15):4847-55. PMID:11939779

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1g5f"

@@ Line 1: / Line 1: @@
 ==STRUCTURE OF LINB COMPLEXED WITH 1,2-DICHLOROETHANE==
 <StructureSection load='1g5f' size='340' side='right' caption='[[1g5f]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1g5f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_devorans"_zimmermann_1890 "bacillus devorans" zimmermann 1890]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G5F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G5F FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1g5f]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G5F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G5F FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DCE:1,2-DICHLOROETHANE'>DCE</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2MR:N3,+N4-DIMETHYLARGININE'>2MR</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1g42|1g42]], [[1g4h|1g4h]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LINB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=13689 "Bacillus devorans" Zimmermann 1890])</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1g5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g5f OCA], [http://pdbe.org/1g5f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1g5f RCSB], [http://www.ebi.ac.uk/pdbsum/1g5f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1g5f ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1g5f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g5f OCA], [http://pdbe.org/1g5f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1g5f RCSB], [http://www.ebi.ac.uk/pdbsum/1g5f PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 19: @@
     <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1g5f ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 37: / Line 37: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus devorans zimmermann 1890]]
 [[Category: Bohac, M]]
 [[Category: Damborsky, J]]

1g5f

From Proteopedia

Revision as of 07:02, 5 April 2017

STRUCTURE OF LINB COMPLEXED WITH 1,2-DICHLOROETHANE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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