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| | ==Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA in complex with 2-propanol== | | ==Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA in complex with 2-propanol== |
| - | <StructureSection load='4e46' size='340' side='right' caption='[[4e46]], [[Resolution|resolution]] 1.26Å' scene=''> | + | <StructureSection load='4e46' size='340' side='right'caption='[[4e46]], [[Resolution|resolution]] 1.26Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4e46]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_mycoides_roseum"_grotenfelt_1889 "bacterium mycoides roseum" grotenfelt 1889]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E46 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E46 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4e46]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_rhodochrous Rhodococcus rhodochrous]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E46 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E46 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3fbw|3fbw]], [[3fwh|3fwh]], [[3g9x|3g9x]], [[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=4e46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e46 OCA], [https://pdbe.org/4e46 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e46 RCSB], [https://www.ebi.ac.uk/pdbsum/4e46 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e46 ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dhaA ([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=4e46 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e46 OCA], [http://pdbe.org/4e46 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e46 RCSB], [http://www.ebi.ac.uk/pdbsum/4e46 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e46 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 4e46" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4e46" 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: Chaloupkova, R]] | + | [[Category: Chaloupkova R]] |
| - | [[Category: Damborsky, J]] | + | [[Category: Damborsky J]] |
| - | [[Category: Smatanova, I Kuta]] | + | [[Category: Kuta Smatanova I]] |
| - | [[Category: Stsiapanava, A]] | + | [[Category: Stsiapanava A]] |
| - | [[Category: Alpha/beta hydrolase fold]]
| + | |
| - | [[Category: Catalytic pentad]]
| + | |
| - | [[Category: Halide binding]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Hydrolytic dehalogenation]]
| + | |
| 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
The use of enzymes for biocatalysis can be significantly enhanced by using organic cosolvents in the reaction mixtures. Selection of the cosolvent type and concentration range for an enzymatic reaction is challenging and requires extensive empirical testing. An understanding of protein-solvent interaction could provide a theoretical framework for rationalising the selection process. Here, the behaviour of three model enzymes (haloalkane dehalogenases) was investigated in the presence of three representative organic cosolvents (acetone, formamide, and isopropanol). Steady-state kinetics assays, molecular dynamics simulations, and time-resolved fluorescence spectroscopy were used to elucidate the molecular mechanisms of enzyme-solvent interactions. Cosolvent molecules entered the enzymes' access tunnels and active sites, enlarged their volumes with no change in overall protein structure, but surprisingly did not act as competitive inhibitors. At low concentrations, the cosolvents either enhanced catalysis by lowering K(0.5) and increasing k(cat), or caused enzyme inactivation by promoting substrate inhibition and decreasing k(cat). The induced activation and inhibition of the enzymes correlated with expansion of the active-site pockets and their occupancy by cosolvent molecules. The study demonstrates that quantitative analysis of the proportions of the access tunnels and active-sites occupied by organic solvent molecules provides the valuable information for rational selection of appropriate protein-solvent pair and effective cosolvent concentration.
Expansion of access tunnels and active-site cavities influence activity of haloalkane dehalogenases in organic cosolvents.,Stepankova V, Khabiri M, Brezovsky J, Pavelka A, Sykora J, Amaro M, Minofar B, Prokop Z, Hof M, Ettrich R, Chaloupkova R, Damborsky J Chembiochem. 2013 May 10;14(7):890-7. doi: 10.1002/cbic.201200733. Epub 2013 Apr , 5. PMID:23564727[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Stepankova V, Khabiri M, Brezovsky J, Pavelka A, Sykora J, Amaro M, Minofar B, Prokop Z, Hof M, Ettrich R, Chaloupkova R, Damborsky J. Expansion of access tunnels and active-site cavities influence activity of haloalkane dehalogenases in organic cosolvents. Chembiochem. 2013 May 10;14(7):890-7. doi: 10.1002/cbic.201200733. Epub 2013 Apr , 5. PMID:23564727 doi:http://dx.doi.org/10.1002/cbic.201200733
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