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6exh

From Proteopedia

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Crystal structure of the complex Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO5 with Fe(II)/succinate/(4R)-4-hydroxy-L-lysine

Structural highlights

6exh is a 4 chain structure with sequence from Flavobacterium sp.. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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]

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Bastard K, Isabet T, Stura EA, Legrand P, Zaparucha A. Structural Studies based on two Lysine Dioxygenases with Distinct Regioselectivity Brings Insights Into Enzyme Specificity within the Clavaminate Synthase-Like Family. Sci Rep. 2018 Nov 8;8(1):16587. doi: 10.1038/s41598-018-34795-9. PMID:30410048 doi:http://dx.doi.org/10.1038/s41598-018-34795-9

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6exh"

@@ Line 3: / Line 3: @@
 <StructureSection load='6exh' size='340' side='right'caption='[[6exh]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6exh]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Flasp Flasp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6EXH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6EXH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6exh]] 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=6EXH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6EXH 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=LYO:4-HYDROXY-LYSINE'>LYO</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]] 2.6&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PMI10_03368 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=239 FLASP])</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=LYO:4-HYDROXY-LYSINE'>LYO</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6exh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6exh OCA], [http://pdbe.org/6exh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6exh RCSB], [http://www.ebi.ac.uk/pdbsum/6exh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6exh 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=6exh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6exh OCA], [https://pdbe.org/6exh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6exh RCSB], [https://www.ebi.ac.uk/pdbsum/6exh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6exh 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 ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 6exh" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
+*[[Hydroxylases 3D structures|Hydroxylases 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Flasp]]
+[[Category: Flavobacterium sp]]
 [[Category: Large Structures]]
-[[Category: Bastard, K]]
+[[Category: Bastard K]]
-[[Category: Isabet, T]]
+[[Category: Isabet T]]
-[[Category: Legrand, P]]
+[[Category: Legrand P]]
-[[Category: Stura, E]]
+[[Category: Stura E]]
-[[Category: Zaparucha, A]]
+[[Category: Zaparucha A]]
-[[Category: Dioxygenase]]
-[[Category: Enzyme]]
-[[Category: Feii alphakg form]]
-[[Category: Oxidoreductase]]
-[[Category: Oxydoreductase]]

6exh

From Proteopedia

Current revision

Crystal structure of the complex Fe(II)/alpha-ketoglutarate dependent dioxygenase KDO5 with Fe(II)/succinate/(4R)-4-hydroxy-L-lysine

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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