1jud: Difference between revisions

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 ==L-2-HALOACID DEHALOGENASE==
-<StructureSection load='1jud' size='340' side='right' caption='[[1jud]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='1jud' size='340' side='right'caption='[[1jud]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1jud]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_sp. Pseudomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JUD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JUD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1jud]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_sp._YL Pseudomonas sp. YL]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JUD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JUD FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">L-DEX YL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=306 Pseudomonas sp.])</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]] 2.5&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/(S)-2-haloacid_dehalogenase (S)-2-haloacid dehalogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.8.1.2 3.8.1.2] </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=1jud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jud OCA], [https://pdbe.org/1jud PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jud RCSB], [https://www.ebi.ac.uk/pdbsum/1jud PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jud ProSAT]</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=1jud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jud OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jud RCSB], [http://www.ebi.ac.uk/pdbsum/1jud PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/HAD_PSEUY HAD_PSEUY]] Catalyzes the hydrolytic dehalogenation of small (S)-2-haloalkanoic acids to yield the corresponding (R)-2-hydroxyalkanoic acids. Acts on acids of short chain lengths, C(2) to C(4), with inversion of configuration at C-2.
+[https://www.uniprot.org/uniprot/HAD_PSEUY HAD_PSEUY] Catalyzes the hydrolytic dehalogenation of small (S)-2-haloalkanoic acids to yield the corresponding (R)-2-hydroxyalkanoic acids. Acts on acids of short chain lengths, C(2) to C(4), with inversion of configuration at C-2.
 == 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/ju/1jud_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ju/1jud_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1jud ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-L-2-Haloacid dehalogenase catalyzes the hydrolytic dehalogenation of L-2-haloalkanoic acids to yield the corresponding D-2-hydroxyalkanoic acids. The crystal structure of the homodimeric enzyme from Pseudomonas sp. YL has been determined by a multiple isomorphous replacement method and refined at 2.5 A resolution to a crystallographic R-factor of 19.5%. The subunit consists of two structurally distinct domains: the core domain and the subdomain. The core domain has an alpha/beta structure formed by a six-stranded parallel beta-sheet flanked by five alpha-helices. The subdomain inserted into the core domain has a four helix bundle structure providing the greater part of the interface for dimer formation. There is an active site cavity between the domains. An experimentally identified nucleophilic residue, Asp-10, is located on a loop following the amino-terminal beta-strand in the core domain, and other functional residues, Thr-14, Arg-41, Ser-118, Lys-151, Tyr-157, Ser-175, Asn-177, and Asp-180, detected by a site-directed mutagenesis experiment, are arranged around the nucleophile in the active site. Although the enzyme is an alpha/beta-type hydrolase, it does not belong to the alpha/beta hydrolase fold family, from the viewpoint of the topological feature and the position of the nucleophile.
-Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp. YL. An alpha/beta hydrolase structure that is different from the alpha/beta hydrolase fold.,Hisano T, Hata Y, Fujii T, Liu JQ, Kurihara T, Esaki N, Soda K J Biol Chem. 1996 Aug 23;271(34):20322-30. PMID:8702766<ref>PMID:8702766</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Dehalogenase|Dehalogenase]]
+*[[Dehalogenase 3D structures|Dehalogenase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Pseudomonas sp]]
+[[Category: Large Structures]]
-[[Category: Esaki, N]]
+[[Category: Pseudomonas sp. YL]]
-[[Category: Fujii, T]]
+[[Category: Esaki N]]
-[[Category: Hata, Y]]
+[[Category: Fujii T]]
-[[Category: Hisano, T]]
+[[Category: Hata Y]]
-[[Category: Kurihara, T]]
+[[Category: Hisano T]]
-[[Category: Liu, J Q]]
+[[Category: Kurihara T]]
-[[Category: Soda, K]]
+[[Category: Liu J-Q]]
-[[Category: Dehalogenase]]
+[[Category: Soda K]]
-[[Category: Hydrolase]]