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| | <StructureSection load='2xt0' size='340' side='right'caption='[[2xt0]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='2xt0' size='340' side='right'caption='[[2xt0]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2xt0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aj_13960 Aj 13960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XT0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XT0 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2xt0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Plesiocystis_pacifica Plesiocystis pacifica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XT0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XT0 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.9Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Haloalkane_dehalogenase Haloalkane dehalogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.5 3.8.1.5] </span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2xt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xt0 OCA], [https://pdbe.org/2xt0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xt0 RCSB], [https://www.ebi.ac.uk/pdbsum/2xt0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xt0 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=2xt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xt0 OCA], [https://pdbe.org/2xt0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xt0 RCSB], [https://www.ebi.ac.uk/pdbsum/2xt0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xt0 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A6G7B1_9DELT A6G7B1_9DELT] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aj 13960]] | |
| - | [[Category: Haloalkane dehalogenase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bogdanovic, X]] | + | [[Category: Plesiocystis pacifica]] |
| - | [[Category: Hinrichs, W]] | + | [[Category: Bogdanovic X]] |
| - | [[Category: Palm, G J]] | + | [[Category: Hinrichs W]] |
| - | [[Category: Alpha-beta hydrolase fold]] | + | [[Category: Palm GJ]] |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
A6G7B1_9DELT
Publication Abstract from PubMed
A haloalkane dehalogenase (DppA) from Plesiocystis pacifica SIR-1 was identified by sequence comparison in the NCBI database, cloned, functionally expressed in Escherichia coli, purified, and biochemically characterized. The three-dimensional (3D) structure was determined by X-ray crystallography and has been refined at 1.95 A resolution to an R-factor of 21.93%. The enzyme is composed of an alpha/beta-hydrolase fold and a cap domain and the overall fold is similar to other known haloalkane dehalogenases. Active site residues were identified as Asp123, His278, and Asp249 and Trp124 and Trp163 as halide-stabilizing residues. DppA, like DhlA from Xanthobacter autotrophicus GJ10, is a member of the haloalkane dehalogenase subfamily HLD-I. As a consequence, these enzymes have in common the relative position of their catalytic residues within the structure and also show some similarities in the substrate specificity. The enzyme shows high preference for 1-bromobutane and does not accept chlorinated alkanes, halo acids, or halo alcohols. It is a monomeric protein with a molecular mass of 32.6 kDa and exhibits maximum activity between 33 and 37 degrees C with a pH optimum between pH 8 and 9. The K(m) and k(cat) values for 1-bromobutane were 24.0 mM and 8.08 s(-1). Furthermore, from the 3D-structure of DppA, it was found that the enzyme possesses a large and open active site pocket. Docking experiments were performed to explain the experimentally determined substrate preferences.
Cloning, functional expression, biochemical characterization, and structural analysis of a haloalkane dehalogenase from Plesiocystis pacifica SIR-1.,Hesseler M, Bogdanovic X, Hidalgo A, Berenguer J, Palm GJ, Hinrichs W, Bornscheuer UT Appl Microbiol Biotechnol. 2011 Aug;91(4):1049-60. Epub 2011 May 21. PMID:21603934[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Hesseler M, Bogdanovic X, Hidalgo A, Berenguer J, Palm GJ, Hinrichs W, Bornscheuer UT. Cloning, functional expression, biochemical characterization, and structural analysis of a haloalkane dehalogenase from Plesiocystis pacifica SIR-1. Appl Microbiol Biotechnol. 2011 Aug;91(4):1049-60. Epub 2011 May 21. PMID:21603934 doi:10.1007/s00253-011-3328-x
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