4k2a

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==Crystal structure of haloalkane dehalogenase DbeA from Bradyrhizobium elkani USDA94==
==Crystal structure of haloalkane dehalogenase DbeA from Bradyrhizobium elkani USDA94==
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<StructureSection load='4k2a' size='340' side='right' caption='[[4k2a]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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<StructureSection load='4k2a' size='340' side='right'caption='[[4k2a]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4k2a]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K2A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K2A FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4k2a]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_elkanii Bradyrhizobium elkanii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K2A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K2A FirstGlance]. <br>
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</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></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3a2m|3a2m]], [[2bn6|2bn6]], [[1cij|1cij]], [[2qvb|2qvb]], [[1cv2|1cv2]]</td></tr>
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<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></td></tr>
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<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>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4k2a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k2a OCA], [https://pdbe.org/4k2a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k2a RCSB], [https://www.ebi.ac.uk/pdbsum/4k2a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k2a ProSAT]</span></td></tr>
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<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=4k2a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k2a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4k2a RCSB], [http://www.ebi.ac.uk/pdbsum/4k2a PDBsum]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/E2RV62_BRAEL E2RV62_BRAEL]] Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons (By similarity).[HAMAP-Rule:MF_01231]
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[https://www.uniprot.org/uniprot/E2RV62_BRAEL E2RV62_BRAEL] Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons (By similarity).[HAMAP-Rule:MF_01231]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The crystal structure of the novel haloalkane dehalogenase DbeA from Bradyrhizobium elkanii USDA94 revealed the presence of two chloride ions buried in the protein interior. The first halide-binding site is involved in substrate binding and is present in all structurally characterized haloalkane dehalogenases. The second halide-binding site is unique to DbeA. To elucidate the role of the second halide-binding site in enzyme functionality, a two-point mutant lacking this site was constructed and characterized. These substitutions resulted in a shift in the substrate-specificity class and were accompanied by a decrease in enzyme activity, stability and the elimination of substrate inhibition. The changes in enzyme catalytic activity were attributed to deceleration of the rate-limiting hydrolytic step mediated by the lower basicity of the catalytic histidine.
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Structural and functional analysis of a novel haloalkane dehalogenase with two halide-binding sites.,Chaloupkova R, Prudnikova T, Rezacova P, Prokop Z, Koudelakova T, Daniel L, Brezovsky J, Ikeda-Ohtsubo W, Sato Y, Kuty M, Nagata Y, Kuta Smatanova I, Damborsky J Acta Crystallogr D Biol Crystallogr. 2014 Jul;70(Pt 7):1884-97. doi:, 10.1107/S1399004714009018. Epub 2014 Jun 29. PMID:25004965<ref>PMID:25004965</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==See Also==
==See Also==
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*[[Dehalogenase|Dehalogenase]]
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*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Haloalkane dehalogenase]]
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[[Category: Bradyrhizobium elkanii]]
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[[Category: Chaloupkova, R]]
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[[Category: Large Structures]]
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[[Category: Damborsky, J]]
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[[Category: Chaloupkova R]]
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[[Category: Koudelakova, T]]
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[[Category: Damborsky J]]
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[[Category: Kuty, M]]
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[[Category: Koudelakova T]]
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[[Category: Mozga, T]]
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[[Category: Kuta Smatanova I]]
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[[Category: Nagata, Y]]
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[[Category: Kuty M]]
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[[Category: Prudnikova, T]]
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[[Category: Mozga T]]
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[[Category: Rezacova, P]]
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[[Category: Nagata Y]]
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[[Category: S2F, Structure 2.Function Project]]
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[[Category: Prudnikova T]]
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[[Category: Sato, Y]]
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[[Category: Rezacova P]]
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[[Category: Smatanova, I Kuta]]
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[[Category: Sato Y]]
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[[Category: Dimer catalytic pentad]]
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[[Category: Enzyme function initiative]]
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[[Category: Halogen binding]]
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[[Category: Hydrolase]]
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[[Category: S2f]]
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[[Category: Structural genomic]]
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[[Category: Structure 2 function project]]
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[[Category: Two domain organization]]
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Current revision

Crystal structure of haloalkane dehalogenase DbeA from Bradyrhizobium elkani USDA94

PDB ID 4k2a

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