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2bfn

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[[Image:2bfn.gif|left|200px]]<br /><applet load="2bfn" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2bfn, resolution 1.600&Aring;" />
 
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'''THE CRYSTAL STRUCTURE OF THE COMPLEX OF THE HALOALKANE DEHALOGENASE LINB WITH THE PRODUCT OF DEHALOGENATION REACTION 1,2-DICHLOROPROPANE.'''<br />
 
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==Overview==
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==The crystal structure of the complex of the haloalkane dehalogenase LinB with the product of dehalogenation reaction 1,2-dichloropropane.==
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1,2,3-Trichloropropane (TCP) is a highly toxic and recalcitrant compound., Haloalkane dehalogenases are bacterial enzymes that catalyze the cleavage, of a carbon-halogen bond in a wide range of organic halogenated compounds., Haloalkane dehalogenase LinB from Sphingobium japonicum UT26 has, for a, long time, been considered inactive with TCP, since the reaction cannot be, easily detected by conventional analytical methods. Here we demonstrate, detection of the weak activity (k(cat) = 0.005 s(-1)) of LinB with TCP, using X-ray crystallography and microcalorimetry. This observation makes, LinB a useful starting material for the development of a new biocatalyst, toward TCP by protein engineering. Microcalorimetry is proposed to be a, universal method for the detection of weak enzymatic activities. Detection, of these activities is becoming increasingly important for engineering, novel biocatalysts using the scaffolds of proteins with promiscuous, activities.
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<StructureSection load='2bfn' size='340' side='right'caption='[[2bfn]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2bfn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_paucimobilis Sphingomonas paucimobilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BFN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BFN FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=D2P:(2S)-2,3-DICHLOROPROPAN-1-OL'>D2P</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bfn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bfn OCA], [https://pdbe.org/2bfn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bfn RCSB], [https://www.ebi.ac.uk/pdbsum/2bfn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bfn ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/LINB_SPHJU LINB_SPHJU] 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 are good substrates (PubMed:9293022, PubMed:10100638). Shows almost no activity with 1,2-dichloroethane, but very high activity with the brominated analog (PubMed:9293022). Is involved in the degradation of the important environmental pollutant gamma-hexachlorocyclohexane (gamma-HCH or 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) (PubMed:7691794). This degradation pathway allows S.japonicum UT26 to grow on gamma-HCH as the sole source of carbon and energy.<ref>PMID:10100638</ref> <ref>PMID:7691794</ref> <ref>PMID:9293022</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bf/2bfn_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2bfn ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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1,2,3-Trichloropropane (TCP) is a highly toxic and recalcitrant compound. Haloalkane dehalogenases are bacterial enzymes that catalyze the cleavage of a carbon-halogen bond in a wide range of organic halogenated compounds. Haloalkane dehalogenase LinB from Sphingobium japonicum UT26 has, for a long time, been considered inactive with TCP, since the reaction cannot be easily detected by conventional analytical methods. Here we demonstrate detection of the weak activity (k(cat) = 0.005 s(-1)) of LinB with TCP using X-ray crystallography and microcalorimetry. This observation makes LinB a useful starting material for the development of a new biocatalyst toward TCP by protein engineering. Microcalorimetry is proposed to be a universal method for the detection of weak enzymatic activities. Detection of these activities is becoming increasingly important for engineering novel biocatalysts using the scaffolds of proteins with promiscuous activities.
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==About this Structure==
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Weak activity of haloalkane dehalogenase LinB with 1,2,3-trichloropropane revealed by X-Ray crystallography and microcalorimetry.,Monincova M, Prokop Z, Vevodova J, Nagata Y, Damborsky J Appl Environ Microbiol. 2007 Mar;73(6):2005-8. Epub 2007 Jan 26. PMID:17259360<ref>PMID:17259360</ref>
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2BFN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=D2P:'>D2P</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Sites: <scene name='pdbsite=AC1:D2p+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Cl+Binding+Site+For+Chain+A'>AC2</scene>, <scene name='pdbsite=AC3:Ca+Binding+Site+For+Chain+A'>AC3</scene>, <scene name='pdbsite=AC4:Ca+Binding+Site+For+Chain+A'>AC4</scene> and <scene name='pdbsite=AC5:Ca+Binding+Site+For+Chain+A'>AC5</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BFN OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Weak activity of haloalkane dehalogenase LinB with 1,2,3-trichloropropane revealed by X-Ray crystallography and microcalorimetry., Monincova M, Prokop Z, Vevodova J, Nagata Y, Damborsky J, Appl Environ Microbiol. 2007 Mar;73(6):2005-8. Epub 2007 Jan 26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17259360 17259360]
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</div>
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[[Category: Single protein]]
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<div class="pdbe-citations 2bfn" style="background-color:#fffaf0;"></div>
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[[Category: Banas, P.]]
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[[Category: Bohac, M.]]
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[[Category: Damborsky, J.]]
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[[Category: Jerabek, P.]]
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[[Category: Otyepka, M.]]
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[[Category: Vevodova, J.]]
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[[Category: CA]]
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[[Category: CL]]
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[[Category: D2P]]
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[[Category: 1]]
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[[Category: 2]]
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[[Category: 3-trichloropropane]]
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[[Category: alpha/beta-hydrolase]]
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[[Category: haloalkane dehalogenase linb]]
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[[Category: hydrolase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Feb 3 10:23:32 2008''
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==See Also==
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*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Sphingomonas paucimobilis]]
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[[Category: Banas P]]
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[[Category: Bohac M]]
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[[Category: Damborsky J]]
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[[Category: Jerabek P]]
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[[Category: Otyepka M]]
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[[Category: Vevodova J]]

Current revision

The crystal structure of the complex of the haloalkane dehalogenase LinB with the product of dehalogenation reaction 1,2-dichloropropane.

PDB ID 2bfn

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