1x42: Difference between revisions
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==Crystal structure of a haloacid dehalogenase family protein (PH0459) from Pyrococcus horikoshii OT3== | |||
<StructureSection load='1x42' size='340' side='right'caption='[[1x42]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1x42]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X42 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1x42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x42 OCA], [https://pdbe.org/1x42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x42 RCSB], [https://www.ebi.ac.uk/pdbsum/1x42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x42 ProSAT], [https://www.topsan.org/Proteins/RSGI/1x42 TOPSAN]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/O58216_PYRHO O58216_PYRHO] | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x4/1x42_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1x42 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
PH0459, from the hyperthermophilic archaeon Pyrococcus horikoshii OT3, is a probable haloacid dehalogenase with a molecular mass of 26,725 Da. Here, we report the 2.0 A crystal structure of PH0459 (PDB ID: 1X42) determined by the multiwavelength anomalous dispersion method. The core domain has an alpha/beta structure formed by a six-stranded parallel beta-sheet flanked by six alpha-helices and three 3(10)-helices. One disulfide bond, Cys186-Cys212, forms a bridge between an alpha-helix and a 3(10)-helix, although PH0459 seems to be an intracellular protein. The subdomain inserted into the core domain has a four-helix bundle structure. The crystal packing suggests that PH0459 exists as a monomer. A structural homology search revealed that PH0459 resembles the l-2-haloacid dehalogenases l-DEX YL from Pseudomonas sp. YL and DhlB from Xanthobacter autotrophicus GJ10. A comparison of the active sites suggested that PH0459 probably has haloacid dehalogenase activity, but its substrate specificity may be different. In addition, the disulfide bond in PH0459 probably facilitates the structural stabilization of the neighboring region in the monomeric form, although the corresponding regions in l-DEX YL and DhlB may be stabilized by dimerization. Since heat-stable dehalogenases can be used for the detoxification of halogenated aliphatic compounds, PH0459 will be a useful target for biotechnological research. | |||
Crystal structure of the probable haloacid dehalogenase PH0459 from Pyrococcus horikoshii OT3.,Arai R, Kukimoto-Niino M, Kuroishi C, Bessho Y, Shirouzu M, Yokoyama S Protein Sci. 2006 Feb;15(2):373-7. Epub 2005 Dec 29. PMID:16385007<ref>PMID:16385007</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1x42" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
== | __TOC__ | ||
< | </StructureSection> | ||
[[Category: Pyrococcus horikoshii]] | [[Category: Large Structures]] | ||
[[Category: Arai | [[Category: Pyrococcus horikoshii OT3]] | ||
[[Category: Kukimoto-Niino | [[Category: Arai R]] | ||
[[Category: Kukimoto-Niino M]] | |||
[[Category: Shirouzu | [[Category: Shirouzu M]] | ||
[[Category: Sugahara | [[Category: Sugahara M]] | ||
[[Category: Yokoyama | [[Category: Yokoyama S]] | ||
Latest revision as of 10:42, 23 October 2024
Crystal structure of a haloacid dehalogenase family protein (PH0459) from Pyrococcus horikoshii OT3Crystal structure of a haloacid dehalogenase family protein (PH0459) from Pyrococcus horikoshii OT3
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedPH0459, from the hyperthermophilic archaeon Pyrococcus horikoshii OT3, is a probable haloacid dehalogenase with a molecular mass of 26,725 Da. Here, we report the 2.0 A crystal structure of PH0459 (PDB ID: 1X42) determined by the multiwavelength anomalous dispersion method. The core domain has an alpha/beta structure formed by a six-stranded parallel beta-sheet flanked by six alpha-helices and three 3(10)-helices. One disulfide bond, Cys186-Cys212, forms a bridge between an alpha-helix and a 3(10)-helix, although PH0459 seems to be an intracellular protein. The subdomain inserted into the core domain has a four-helix bundle structure. The crystal packing suggests that PH0459 exists as a monomer. A structural homology search revealed that PH0459 resembles the l-2-haloacid dehalogenases l-DEX YL from Pseudomonas sp. YL and DhlB from Xanthobacter autotrophicus GJ10. A comparison of the active sites suggested that PH0459 probably has haloacid dehalogenase activity, but its substrate specificity may be different. In addition, the disulfide bond in PH0459 probably facilitates the structural stabilization of the neighboring region in the monomeric form, although the corresponding regions in l-DEX YL and DhlB may be stabilized by dimerization. Since heat-stable dehalogenases can be used for the detoxification of halogenated aliphatic compounds, PH0459 will be a useful target for biotechnological research. Crystal structure of the probable haloacid dehalogenase PH0459 from Pyrococcus horikoshii OT3.,Arai R, Kukimoto-Niino M, Kuroishi C, Bessho Y, Shirouzu M, Yokoyama S Protein Sci. 2006 Feb;15(2):373-7. Epub 2005 Dec 29. PMID:16385007[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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