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==Structure of Rhodococcus rhodochrous haloalkane dehalogenase mutant DhaA31==
==Structure of Rhodococcus rhodochrous haloalkane dehalogenase mutant DhaA31==
<StructureSection load='3rk4' size='340' side='right' caption='[[3rk4]], [[Resolution|resolution]] 1.31&Aring;' scene=''>
<StructureSection load='3rk4' size='340' side='right'caption='[[3rk4]], [[Resolution|resolution]] 1.31&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3rk4]] 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=3RK4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RK4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3rk4]] 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=3RK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RK4 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.31&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3fbw|3fbw]], [[3g9x|3g9x]], [[3fwh|3fwh]], [[1bn6|1bn6]], [[1cqw|1cqw]], [[3rlt|3rlt]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3rk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rk4 OCA], [https://pdbe.org/3rk4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rk4 RCSB], [https://www.ebi.ac.uk/pdbsum/3rk4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rk4 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=3rk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rk4 OCA], [http://pdbe.org/3rk4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rk4 RCSB], [http://www.ebi.ac.uk/pdbsum/3rk4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rk4 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;">
== 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<ref>PMID:24531456</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3rk4" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Dehalogenase|Dehalogenase]]
*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
== 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: 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: Halide binding]]
[[Category: Hydrolase]]
[[Category: Hydrolytic dehalogenation]]

Latest revision as of 15:27, 14 March 2024

Structure of Rhodococcus rhodochrous haloalkane dehalogenase mutant DhaA31Structure of Rhodococcus rhodochrous haloalkane dehalogenase mutant DhaA31

Structural highlights

3rk4 is a 1 chain structure with sequence from Rhodococcus rhodochrous. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.31Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

See Also

3rk4, resolution 1.31Å

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