4e46 - Revision history

OCA at 14:52, 14 March 2024

2024-03-14T14:52:04Z

← Older revision		Revision as of 14:52, 14 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<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>		<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" 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>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.26Å</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='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='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>
	</table>		</table>
	== Function ==		== Function ==
	[[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.		[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;">~~
	~~== 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<ref>PMID:23564727</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 4e46" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Dehalogenase 3D structures\|Dehalogenase 3D structures]]		*[[Dehalogenase 3D structures\|Dehalogenase 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:48, 28 September 2022

2022-09-28T06:48:59Z

← Older revision		Revision as of 06:48, 28 September 2022
Line 1:		Line 1:

	==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 ==
Line 21:		Line 18:
	</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~~]]

OCA at 07:59, 15 November 2017

2017-11-15T07:59:02Z

← Older revision		Revision as of 07:59, 15 November 2017
Line 21:		Line 21:
	</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\|Dehalogenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:04, 11 August 2016

2016-08-11T16:04:17Z

← Older revision		Revision as of 16:04, 11 August 2016
Line 1:		Line 1:

	==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=''>
Line 7:		Line 8:
	<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='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='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://www.rcsb.org/pdb/explore.do?structureId=4e46 RCSB], [http://www.ebi.ac.uk/pdbsum/4e46 PDBsum]</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 ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 4e46" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 07:45, 14 January 2015

2015-01-14T07:45:56Z

← Older revision		Revision as of 07:45, 14 January 2015
Line 2:		Line 2:
	<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/~~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 [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 [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>
	</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"><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='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='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 ~~Rhodococcus rhodochrous~~])</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='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://www.rcsb.org/pdb/explore.do?structureId=4e46 RCSB], [http://www.ebi.ac.uk/pdbsum/4e46 PDBsum]</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://www.rcsb.org/pdb/explore.do?structureId=4e46 RCSB], [http://www.ebi.ac.uk/pdbsum/4e46 PDBsum]</span></td></tr>
Line 11:		Line 11:
	== 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.		[[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.
			<div style="background-color:#fffaf0;">
			== 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<ref>PMID:23564727</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>

	==See Also==		==See Also==
	*[[Dehalogenase\|Dehalogenase]]		*[[Dehalogenase\|Dehalogenase]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Bacterium mycoides roseum grotenfelt 1889]]
	[[Category: Haloalkane dehalogenase]]		[[Category: Haloalkane dehalogenase]]
	~~[[Category: Rhodococcus rhodochrous]]~~
	[[Category: Chaloupkova, R]]		[[Category: Chaloupkova, R]]
	[[Category: Damborsky, J]]		[[Category: Damborsky, J]]

OCA at 20:05, 25 December 2014

2014-12-25T20:05:11Z

← Older revision		Revision as of 20:05, 25 December 2014
Line 1:		Line 1:
	~~{{STRUCTURE_4e46\| PDB=4e46 \| SCENE= }}~~		==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=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4e46]] is a 1 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/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>
			<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='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 Rhodococcus rhodochrous])</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://www.rcsb.org/pdb/explore.do?structureId=4e46 RCSB], [http://www.ebi.ac.uk/pdbsum/4e46 PDBsum]</span></td></tr>
			</table>
			== 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.

	==~~About this Structure~~==		==See Also==
	[[~~4e46~~]] ~~is a 1 chain structure with sequence from [http://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].~~		*[[Dehalogenase\|Dehalogenase]]
			__TOC__
			</StructureSection>
	[[Category: Haloalkane dehalogenase]]		[[Category: Haloalkane dehalogenase]]
	[[Category: Rhodococcus rhodochrous]]		[[Category: Rhodococcus rhodochrous]]
	[[Category: Chaloupkova, R.]]		[[Category: Chaloupkova, R]]
	[[Category: Damborsky, J.]]		[[Category: Damborsky, J]]
	[[Category: Smatanova, I Kuta.]]		[[Category: Smatanova, I Kuta]]
	[[Category: Stsiapanava, A.]]		[[Category: Stsiapanava, A]]
	[[Category: Alpha/beta hydrolase fold]]		[[Category: Alpha/beta hydrolase fold]]
	[[Category: Catalytic pentad]]		[[Category: Catalytic pentad]]

OCA at 10:28, 13 March 2013

2013-03-13T10:28:29Z

← Older revision		Revision as of 10:28, 13 March 2013
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	~~'''Unreleased structure'''~~		{{STRUCTURE_4e46\| PDB=4e46 \| SCENE= }}
			===Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA in complex with 2-propanol===

	~~The entry~~ 4e46 is ~~ON HOLD until Mar 13 2014~~		==About this Structure==
			[[4e46]] is a 1 chain structure with sequence from [http://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].
	~~Authors~~: ~~Stsiapanava, A.,~~ Chaloupkova, R., Damborsky, J.~~, Kuta~~ Smatanova, I.		[[Category: Haloalkane dehalogenase]]
			[[Category: Rhodococcus rhodochrous]]
	~~Description~~: ~~Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA in complex with 2-propanol~~		[[Category: Chaloupkova, R.]]
			[[Category: Damborsky, J.]]
			[[Category: Smatanova, I Kuta.]]
			[[Category: Stsiapanava, A.]]
			[[Category: Alpha/beta hydrolase fold]]
			[[Category: Catalytic pentad]]
			[[Category: Halide binding]]
			[[Category: Hydrolase]]
			[[Category: Hydrolytic dehalogenation]]

OCA at 11:00, 23 January 2013

2013-01-23T11:00:26Z

← Older revision		Revision as of 11:00, 23 January 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4e46 is ON HOLD until ~~Paper Publication~~		The entry 4e46 is ON HOLD until Mar 13 2014

	Authors: Stsiapanava, A., Chaloupkova, R., Damborsky, J., Kuta Smatanova, I.		Authors: Stsiapanava, A., Chaloupkova, R., Damborsky, J., Kuta Smatanova, I.

	Description: Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA in complex with 2-propanol		Description: Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA in complex with 2-propanol

OCA at 07:21, 28 March 2012

2012-03-28T07:21:50Z

← Older revision		Revision as of 07:21, 28 March 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4e46 is ON HOLD		The entry 4e46 is ON HOLD until Paper Publication

	Authors: Stsiapanava, A., Chaloupkova, R., Damborsky, J., Kuta Smatanova, I.		Authors: Stsiapanava, A., Chaloupkova, R., Damborsky, J., Kuta Smatanova, I.

	Description: Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA in complex with 2-propanol		Description: Structure of Rhodococcus rhodochrous haloalkane dehalogenase DhaA in complex with 2-propanol

OCA: Protected "4e46" [edit=sysop:move=sysop]

2012-03-21T07:16:32Z

Protected "4e46" [edit=sysop:move=sysop]

← Older revision	Revision as of 07:16, 21 March 2012
(No difference)