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| | ==Crystal structure of haloalkane dehalogenase LinB from Sphingobium sp. MI1205== | | ==Crystal structure of haloalkane dehalogenase LinB from Sphingobium sp. MI1205== |
| - | <StructureSection load='4h77' size='340' side='right' caption='[[4h77]], [[Resolution|resolution]] 1.60Å' scene=''> | + | <StructureSection load='4h77' size='340' side='right'caption='[[4h77]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4h77]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Sphingobium_sp._mi1205 Sphingobium sp. mi1205]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H77 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H77 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4h77]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingobium_sp._MI1205 Sphingobium sp. MI1205]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H77 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H77 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=GOL:GLYCEROL'>GOL</scene></td></tr> | + | </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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4h7d|4h7d]], [[4h7e|4h7e]], [[4h7f|4h7f]], [[4h7h|4h7h]], [[4h7i|4h7i]], [[4h7j|4h7j]], [[4h7k|4h7k]]</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=GOL:GLYCEROL'>GOL</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">linB, dhaA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=407020 Sphingobium sp. MI1205])</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=4h77 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h77 OCA], [https://pdbe.org/4h77 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h77 RCSB], [https://www.ebi.ac.uk/pdbsum/4h77 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h77 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </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=4h77 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h77 OCA], [http://pdbe.org/4h77 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4h77 RCSB], [http://www.ebi.ac.uk/pdbsum/4h77 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4h77 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A4PEU6_9SPHN A4PEU6_9SPHN]] Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons (By similarity).[HAMAP-Rule:MF_01231] | + | [https://www.uniprot.org/uniprot/A4PEU6_9SPHN A4PEU6_9SPHN] Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons (By similarity).[HAMAP-Rule:MF_01231] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Dehalogenase|Dehalogenase]] | + | *[[Dehalogenase 3D structures|Dehalogenase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Haloalkane dehalogenase]] | + | [[Category: Large Structures]] |
| - | [[Category: Sphingobium sp. mi1205]] | + | [[Category: Sphingobium sp. MI1205]] |
| - | [[Category: Imai, F L]] | + | [[Category: Imai FL]] |
| - | [[Category: Mase, T]] | + | [[Category: Mase T]] |
| - | [[Category: Moriuchi, R]] | + | [[Category: Moriuchi R]] |
| - | [[Category: Nagata, K]] | + | [[Category: Nagata K]] |
| - | [[Category: Nagata, Y]] | + | [[Category: Nagata Y]] |
| - | [[Category: Ohtsuka, J]] | + | [[Category: Ohtsuka J]] |
| - | [[Category: Okai, M]] | + | [[Category: Okai M]] |
| - | [[Category: Tanokura, M]] | + | [[Category: Tanokura M]] |
| - | [[Category: Tsuda, M]] | + | [[Category: Tsuda M]] |
| - | [[Category: Alpha/beta hydrolase fold]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
A4PEU6_9SPHN Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons (By similarity).[HAMAP-Rule:MF_01231]
Publication Abstract from PubMed
The enzymes LinBUT and LinBMI (LinB from Sphingobium japonicum UT26 and Sphingobium sp. MI1205, respectively) catalyze the hydrolytic dechlorination of beta-hexachlorocyclohexane (beta-HCH) and yield different products, 2,3,4,5,6-pentachlorocyclohexanol (PCHL) and 2,3,5,6-tetrachlorocyclohexane-1,4-diol (TCDL), respectively, despite their 98% identity in amino acid sequence. To reveal the structural basis of their different enzymatic properties, we performed site-directed mutagenesis and X-ray crystallographic studies of LinBMI and its seven point mutants. The mutation analysis revealed that the seven amino acid residues uniquely found in LinBMI were categorized into three groups based on the efficiency of the first-step (from beta-HCH to PCHL) and second-step (from PCHL to TCDL) conversions. Crystal structure analyses of wild-type LinBMI and its seven point mutants indicated how each mutated residue contributed to the first- and second-step conversions by LinBMI. The dynamics simulation analyses of wild-type LinBMI and LinBUT revealed that the entrance of the substrate access tunnel of LinBUT was more flexible than that of LinBMI, which could lead to the different efficiencies of dehalogenation activity between these dehalogenases.
Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp. Strain MI1205.,Okai M, Ohtsuka J, Imai LF, Mase T, Moriuchi R, Tsuda M, Nagata K, Nagata Y, Tanokura M J Bacteriol. 2013 Jun;195(11):2642-51. doi: 10.1128/JB.02020-12. Epub 2013 Apr 5. PMID:23564170[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Okai M, Ohtsuka J, Imai LF, Mase T, Moriuchi R, Tsuda M, Nagata K, Nagata Y, Tanokura M. Crystal Structure and Site-Directed Mutagenesis Analyses of Haloalkane Dehalogenase LinB from Sphingobium sp. Strain MI1205. J Bacteriol. 2013 Jun;195(11):2642-51. doi: 10.1128/JB.02020-12. Epub 2013 Apr 5. PMID:23564170 doi:10.1128/JB.02020-12
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