1k5p: Difference between revisions
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<StructureSection load='1k5p' size='340' side='right'caption='[[1k5p]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='1k5p' size='340' side='right'caption='[[1k5p]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1k5p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[1k5p]] 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=1K5P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K5P FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1k5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k5p OCA], [https://pdbe.org/1k5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k5p RCSB], [https://www.ebi.ac.uk/pdbsum/1k5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k5p ProSAT]</span></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=1k5p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k5p OCA], [https://pdbe.org/1k5p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k5p RCSB], [https://www.ebi.ac.uk/pdbsum/1k5p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k5p ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == 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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Sphingomonas paucimobilis]] | ||
[[Category: | [[Category: Damborsky J]] | ||
[[Category: Streltsov VA]] | |||
[[Category: | [[Category: Wilce MCJ]] | ||
[[Category: | |||
Latest revision as of 10:16, 25 October 2023
Hydrolytic haloalkane dehalogenase LINB from sphingomonas paucimobilis UT26 at 1.8A resolutionHydrolytic haloalkane dehalogenase LINB from sphingomonas paucimobilis UT26 at 1.8A resolution
Structural highlights
FunctionLINB_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.[1] [2] [3] 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 PubMedThe 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. 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[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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