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| | ==Structure of Rhodococcus rhodochrous haloalkane dehalogenase mutant DhaA31 in complex with 1, 2, 3 - trichloropropane== | | ==Structure of Rhodococcus rhodochrous haloalkane dehalogenase mutant DhaA31 in complex with 1, 2, 3 - trichloropropane== |
| - | <StructureSection load='4fwb' size='340' side='right' caption='[[4fwb]], [[Resolution|resolution]] 1.26Å' scene=''> | + | <StructureSection load='4fwb' size='340' side='right'caption='[[4fwb]], [[Resolution|resolution]] 1.26Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4fwb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_mycoides_roseum"_grotenfelt_1889 "bacterium mycoides roseum" grotenfelt 1889]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3rlt 3rlt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FWB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FWB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4fwb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_rhodochrous Rhodococcus rhodochrous]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3rlt 3rlt]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FWB FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3KP:1,2,3-TRICHLOROPROPANE'>3KP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3KP:1,2,3-TRICHLOROPROPANE'>3KP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3rk4|3rk4]], [[3fbw|3fbw]], [[3g9x|3g9x]], [[3fwh|3fwh]], [[1bn6|1bn6]], [[1cqw|1cqw]]</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=4fwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fwb OCA], [https://pdbe.org/4fwb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fwb RCSB], [https://www.ebi.ac.uk/pdbsum/4fwb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fwb ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dhaA, DhaA31 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1829 "Bacterium mycoides roseum" Grotenfelt 1889])</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=4fwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fwb OCA], [http://pdbe.org/4fwb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fwb RCSB], [http://www.ebi.ac.uk/pdbsum/4fwb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fwb ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DHAA_RHORH DHAA_RHORH]] Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons. Expresses halogenase activity against 1-chloroalkanes of chain length C3 to C10, and also shows a very weak activity with 1,2-dichloroethane. | + | [https://www.uniprot.org/uniprot/DHAA_RHORH DHAA_RHORH] Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons. Expresses halogenase activity against 1-chloroalkanes of chain length C3 to C10, and also shows a very weak activity with 1,2-dichloroethane. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4fwb" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4fwb" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Dehalogenase 3D structures|Dehalogenase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacterium mycoides roseum grotenfelt 1889]] | + | [[Category: Large Structures]] |
| - | [[Category: Haloalkane dehalogenase]] | + | [[Category: Rhodococcus rhodochrous]] |
| - | [[Category: Lahoda, M]] | + | [[Category: Kuta Smatanova I]] |
| - | [[Category: Mesters, J]] | + | [[Category: Lahoda M]] |
| - | [[Category: Smatanova, I Kuta]] | + | [[Category: Mesters J]] |
| - | [[Category: Stsiapanava, A]] | + | [[Category: Stsiapanava A]] |
| - | [[Category: Alpha/beta hydrolase fold]]
| + | |
| - | [[Category: Catalytic pentad]]
| + | |
| - | [[Category: Enzyme function initiative]]
| + | |
| - | [[Category: Halide binding]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Hydrolytic dehalogenation]]
| + | |
| - | [[Category: Structural genomic]]
| + | |
| Structural highlights
Function
DHAA_RHORH Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons. Expresses halogenase activity against 1-chloroalkanes of chain length C3 to C10, and also shows a very weak activity with 1,2-dichloroethane.
Publication Abstract from PubMed
Haloalkane dehalogenases catalyze the hydrolytic cleavage of carbon-halogen bonds, which is a key step in the aerobic mineralization of many environmental pollutants. One important pollutant is the toxic and anthropogenic compound 1,2,3-trichloropropane (TCP). Rational design was combined with saturation mutagenesis to obtain the haloalkane dehalogenase variant DhaA31, which displays an increased catalytic activity towards TCP. Here, the 1.31 A resolution crystal structure of substrate-free DhaA31, the 1.26 A resolution structure of DhaA31 in complex with TCP and the 1.95 A resolution structure of wild-type DhaA are reported. Crystals of the enzyme-substrate complex were successfully obtained by adding volatile TCP to the reservoir after crystallization at pH 6.5 and room temperature. Comparison of the substrate-free structure with that of the DhaA31 enzyme-substrate complex reveals that the nucleophilic Asp106 changes its conformation from an inactive to an active state during the catalytic cycle. The positions of three chloride ions found inside the active site of the enzyme indicate a possible pathway for halide release from the active site through the main tunnel. Comparison of the DhaA31 variant with wild-type DhaA revealed that the introduced substitutions reduce the volume and the solvent-accessibility of the active-site pocket.
Crystallographic analysis of 1,2,3-trichloropropane biodegradation by the haloalkane dehalogenase DhaA31.,Lahoda M, Mesters JR, Stsiapanava A, Chaloupkova R, Kuty M, Damborsky J, Kuta Smatanova I Acta Crystallogr D Biol Crystallogr. 2014 Feb;70(Pt 2):209-17. doi:, 10.1107/S1399004713026254. Epub 2014 Jan 17. PMID:24531456[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Lahoda M, Mesters JR, Stsiapanava A, Chaloupkova R, Kuty M, Damborsky J, Kuta Smatanova I. Crystallographic analysis of 1,2,3-trichloropropane biodegradation by the haloalkane dehalogenase DhaA31. Acta Crystallogr D Biol Crystallogr. 2014 Feb;70(Pt 2):209-17. doi:, 10.1107/S1399004713026254. Epub 2014 Jan 17. PMID:24531456 doi:http://dx.doi.org/10.1107/S1399004713026254
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