6exf: Difference between revisions

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 ==Crystal structure of the complex Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO5 with Fe(II)/Lysine==
-<StructureSection load='6exf' size='340' side='right' caption='[[6exf]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+<StructureSection load='6exf' size='340' side='right'caption='[[6exf]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6exf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EXF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EXF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6exf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Flavobacterium_sp. Flavobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EXF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6EXF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</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]] 1.95&#8491;</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=6exf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6exf OCA], [http://pdbe.org/6exf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6exf RCSB], [http://www.ebi.ac.uk/pdbsum/6exf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6exf ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LYS:LYSINE'>LYS</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=6exf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6exf OCA], [https://pdbe.org/6exf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6exf RCSB], [https://www.ebi.ac.uk/pdbsum/6exf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6exf ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/LYS4O_FLASC LYS4O_FLASC]] Alpha-ketoglutarate-dependent dioxygenase that in vitro catalyzes the regio- and stereoselective hydroxylation of L-lysine, leading to (4R)-4-hydroxy-L-lysine.[REFERENCE:2]
+[https://www.uniprot.org/uniprot/LYS4O_FLASC LYS4O_FLASC] Alpha-ketoglutarate-dependent dioxygenase that in vitro catalyzes the regio- and stereoselective hydroxylation of L-lysine, leading to (4R)-4-hydroxy-L-lysine.[REFERENCE:2]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Iron(II)/alpha-ketoacid-dependent oxygenases (alphaKAOs) are enzymes that catalyze the oxidation of unactivated C-H bonds, mainly through hydroxylation. Among these, those that are active towards amino-acids and their derivatives are grouped in the Clavaminate Synthase Like (CSL) family. CSL enzymes exhibit high regio- and stereoselectivities with strict substrate specificity. This study reports the structural elucidation of two new regiodivergent members, KDO1 and KDO5, active towards lysine, and the structural and computational analysis of the whole family through modelling and classification of active sites. The structures of KDO1 and KDO5 in complex with their ligands show that one exact position in the active site controls the regioselectivity of the reaction. Our results suggest that the substrate specificity and high stereoselectivity typical of this family is linked to a lid that closes up in order to form a sub-pocket around the side chain of the substrate. This dynamic lid is found throughout the family with varying sequence and length and is associated with a conserved stable dimeric interface. Results from this study could be a starting-point for exploring the functional diversity of the CSL family and direct in vitro screening in the search for new enzymatic activities.
+Structural Studies based on two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity within the Clavaminate Synthase-Like Family.,Bastard K, Isabet T, Stura EA, Legrand P, Zaparucha A Sci Rep. 2018 Nov 8;8(1):16587. doi: 10.1038/s41598-018-34795-9. PMID:30410048<ref>PMID:30410048</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 6exf" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
+*[[Hydroxylases 3D structures|Hydroxylases 3D structures]]
+== References ==
+<references/>
 __TOC__
 </StructureSection>
-[[Category: Bastard, K]]
+[[Category: Flavobacterium sp]]
-[[Category: Isabet, T]]
+[[Category: Large Structures]]
-[[Category: Legrand, P]]
+[[Category: Bastard K]]
-[[Category: Stura, E]]
+[[Category: Isabet T]]
-[[Category: Zaparucha, A]]
+[[Category: Legrand P]]
-[[Category: Dioxygenase]]
+[[Category: Stura E]]
-[[Category: Enzyme]]
+[[Category: Zaparucha A]]
-[[Category: Feii lysine form]]
-[[Category: Oxidoreductase]]