2bfn
From Proteopedia
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| - | [[Image:2bfn.png|left|200px]] | ||
| - | + | ==The crystal structure of the complex of the haloalkane dehalogenase LinB with the product of dehalogenation reaction 1,2-dichloropropane.== | |
| + | <StructureSection load='2bfn' size='340' side='right'caption='[[2bfn]], [[Resolution|resolution]] 1.60Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <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> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> | ||
| + | <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> | ||
| + | <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> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [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> | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bf/2bfn_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
| + | <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/main_output.php?pdb_ID=2bfn ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | 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. | ||
| - | + | 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> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 2bfn" style="background-color:#fffaf0;"></div> | ||
| - | == | + | ==See Also== |
| - | [[ | + | *[[Dehalogenase 3D structures|Dehalogenase 3D structures]] |
| - | + | == References == | |
| - | == | + | <references/> |
| - | < | + | __TOC__ |
| - | [[Category: | + | </StructureSection> |
| + | [[Category: Large Structures]] | ||
[[Category: Sphingomonas paucimobilis]] | [[Category: Sphingomonas paucimobilis]] | ||
| - | [[Category: Banas | + | [[Category: Banas P]] |
| - | [[Category: Bohac | + | [[Category: Bohac M]] |
| - | [[Category: Damborsky | + | [[Category: Damborsky J]] |
| - | [[Category: Jerabek | + | [[Category: Jerabek P]] |
| - | [[Category: Otyepka | + | [[Category: Otyepka M]] |
| - | [[Category: Vevodova | + | [[Category: Vevodova J]] |
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Current revision
The crystal structure of the complex of the haloalkane dehalogenase LinB with the product of dehalogenation reaction 1,2-dichloropropane.
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