6f6j: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==Crystal structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO1 with Fe(II)/succinate/(3S)-3-hydroxy-L-lysine== | ==Crystal structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO1 with Fe(II)/succinate/(3S)-3-hydroxy-L-lysine== | ||
<StructureSection load='6f6j' size='340' side='right' caption='[[6f6j]], [[Resolution|resolution]] 2.00Å' scene=''> | <StructureSection load='6f6j' size='340' side='right'caption='[[6f6j]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6f6j]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F6J OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6f6j]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Catenulispora_acidiphila_DSM_44928 Catenulispora acidiphila DSM 44928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6F6J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6F6J FirstGlance]. <br> | ||
</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=CUW:(2~{S},3~{R})-2,6-bis(azanyl)-3-oxidanyl-hexanoic+acid'>CUW</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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]] 2Å</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <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=CUW:(2~{S},3~{R})-2,6-bis(azanyl)-3-oxidanyl-hexanoic+acid'>CUW</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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=6f6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6f6j OCA], [https://pdbe.org/6f6j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6f6j RCSB], [https://www.ebi.ac.uk/pdbsum/6f6j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6f6j ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/LYS3O_CATAD LYS3O_CATAD] Alpha-ketoglutarate-dependent dioxygenase that in vitro catalyzes the regio- and stereoselective hydroxylation of L-lysine, leading to (3S)-3-hydroxy-L-lysine. Can also use (5R)-5-hydroxy-L-lysine as substrate, but neither D-lysine nor L-ornithine.[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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6f6j" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Dioxygenase 3D structures|Dioxygenase 3D structures]] | |||
*[[Hydroxylases 3D structures|Hydroxylases 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Catenulispora acidiphila DSM 44928]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Bastard K]] | ||
[[Category: | [[Category: Isabet T]] | ||
[[Category: | [[Category: Legrand P]] | ||
[[Category: | [[Category: Stura EA]] | ||
[[Category: | [[Category: Zaparucha A]] | ||
Latest revision as of 13:22, 15 November 2023
Crystal structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO1 with Fe(II)/succinate/(3S)-3-hydroxy-L-lysineCrystal structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO1 with Fe(II)/succinate/(3S)-3-hydroxy-L-lysine
Structural highlights
FunctionLYS3O_CATAD Alpha-ketoglutarate-dependent dioxygenase that in vitro catalyzes the regio- and stereoselective hydroxylation of L-lysine, leading to (3S)-3-hydroxy-L-lysine. Can also use (5R)-5-hydroxy-L-lysine as substrate, but neither D-lysine nor L-ornithine.[REFERENCE:2] Publication Abstract from PubMedIron(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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||