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| | <StructureSection load='3wi7' size='340' side='right'caption='[[3wi7]], [[Resolution|resolution]] 1.70Å' scene=''> | | <StructureSection load='3wi7' size='340' side='right'caption='[[3wi7]], [[Resolution|resolution]] 1.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3wi7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrfc Agrfc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WI7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WI7 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3wi7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WI7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WI7 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</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]] 1.7Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wib|3wib]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dhaA, dha, Atu6064, AGR_pTi_130 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=176299 AGRFC])</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>
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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=3wi7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wi7 OCA], [https://pdbe.org/3wi7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wi7 RCSB], [https://www.ebi.ac.uk/pdbsum/3wi7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wi7 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=3wi7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wi7 OCA], [https://pdbe.org/3wi7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wi7 RCSB], [https://www.ebi.ac.uk/pdbsum/3wi7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wi7 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/DHAA_AGRT5 DHAA_AGRT5]] 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).
| + | [https://www.uniprot.org/uniprot/DHAA_AGRFC DHAA_AGRFC] Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons.[HAMAP-Rule:MF_01231] |
| | <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: Agrfc]] | + | [[Category: Agrobacterium fabrum str. C58]] |
| - | [[Category: Haloalkane dehalogenase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Guan, L J]] | + | [[Category: Guan LJ]] |
| - | [[Category: Ohtsuka, J]] | + | [[Category: Ohtsuka J]] |
| - | [[Category: Okai, M]] | + | [[Category: Okai M]] |
| - | [[Category: Tanokura, M]] | + | [[Category: Tanokura M]] |
| - | [[Category: Yabuki, H]] | + | [[Category: Yabuki H]] |
| - | [[Category: Hydrolase]]
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| - | [[Category: Hydrolase fold family]]
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| Structural highlights
Function
DHAA_AGRFC Catalyzes hydrolytic cleavage of carbon-halogen bonds in halogenated aliphatic compounds, leading to the formation of the corresponding primary alcohols, halide ions and protons.[HAMAP-Rule:MF_01231]
Publication Abstract from PubMed
A novel haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58 belongs to the HLD-II subfamily and hydrolyzes brominated and iodinated compounds, leading to the generation of the corresponding alcohol, a halide ion, and a proton. Because DatA possesses a unique Asn-Tyr pair instead of the Asn-Trp pair conserved among the subfamily members, which was proposed to keep the released halide ion stable, the structural basis for its reaction mechanism should be elucidated. Here, we determined the crystal structures of DatA and its Y109W mutant at 1.70 and 1.95 A, respectively, and confirmed the location of the active site by using its novel competitive inhibitor. The structural information from these two crystal structures and the docking simulation suggested that (i) the replacement of the Asn-Tyr pair with the Asn-Trp pair increases the binding affinity for some halogenated compounds, such as 1,3-dibromopropane, mainly due to the electrostatic interaction between Trp109 and halogenated compounds and the change of substrate-binding mode caused by the interaction and (ii) the primary halide-stabilizing residue is only Asn43 in the wild-type DatA, while Tyr109 is a secondary halide-stabilizing residue. Furthermore, docking simulation using the crystal structures of DatA indicated that its enantioselectivity is determined by the large and small spaces around the halogen-binding site.
Crystal structure of the novel haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58 reveals a special halide-stabilizing pair and enantioselectivity mechanism.,Guan L, Yabuki H, Okai M, Ohtsuka J, Tanokura M Appl Microbiol Biotechnol. 2014 Apr 29. PMID:24770384[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Guan L, Yabuki H, Okai M, Ohtsuka J, Tanokura M. Crystal structure of the novel haloalkane dehalogenase DatA from Agrobacterium tumefaciens C58 reveals a special halide-stabilizing pair and enantioselectivity mechanism. Appl Microbiol Biotechnol. 2014 Apr 29. PMID:24770384 doi:http://dx.doi.org/10.1007/s00253-014-5751-2
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