5equ: Difference between revisions
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<StructureSection load='5equ' size='340' side='right'caption='[[5equ]], [[Resolution|resolution]] 2.20Å' scene=''> | <StructureSection load='5equ' size='340' side='right'caption='[[5equ]], [[Resolution|resolution]] 2.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5equ]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[5equ]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_nogalater Streptomyces nogalater]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EQU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EQU FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5R6:NOGALAMYCIN+RO'>5R6</scene>, <scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5R6:NOGALAMYCIN+RO'>5R6</scene>, <scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</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=5equ FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5equ OCA], [https://pdbe.org/5equ PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5equ RCSB], [https://www.ebi.ac.uk/pdbsum/5equ PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5equ ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/Q9RN67_STRNO Q9RN67_STRNO] [https://www.uniprot.org/uniprot/Q9EYI0_STRNO Q9EYI0_STRNO] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Lindqvist | [[Category: Streptomyces nogalater]] | ||
[[Category: Metsa-Ketela | [[Category: Lindqvist Y]] | ||
[[Category: Schneider | [[Category: Metsa-Ketela M]] | ||
[[Category: Selvaraj | [[Category: Schneider G]] | ||
[[Category: Siitonen | [[Category: Selvaraj B]] | ||
[[Category: Siitonen V]] | |||
Latest revision as of 11:17, 12 July 2023
Crystal structure of the epimerase SnoN in complex with Fe3+, alpha ketoglutarate and nogalamycin ROCrystal structure of the epimerase SnoN in complex with Fe3+, alpha ketoglutarate and nogalamycin RO
Structural highlights
FunctionPublication Abstract from PubMedNogalamycin, an aromatic polyketide displaying high cytotoxicity, has a unique structure, with one of the carbohydrate units covalently attached to the aglycone via an additional carbon-carbon bond. The underlying chemistry, which implies a particularly challenging reaction requiring activation of an aliphatic carbon atom, has remained enigmatic. Here, we show that the unusual C5-C2 carbocyclization is catalyzed by the non-heme iron alpha-ketoglutarate (alpha-KG)-dependent SnoK in the biosynthesis of the anthracycline nogalamycin. The data are consistent with a mechanistic proposal whereby the Fe(IV) = O center abstracts the H5 atom from the amino sugar of the substrate, with subsequent attack of the aromatic C2 carbon on the radical center. We further show that, in the same metabolic pathway, the homologous SnoN (38% sequence identity) catalyzes an epimerization step at the adjacent C4 carbon, most likely via a radical mechanism involving the Fe(IV) = O center. SnoK and SnoN have surprisingly similar active site architectures considering the markedly different chemistries catalyzed by the enzymes. Structural studies reveal that the differences are achieved by minor changes in the alignment of the substrates in front of the reactive ferryl-oxo species. Our findings significantly expand the repertoire of reactions reported for this important protein family and provide an illustrative example of enzyme evolution. Divergent non-heme iron enzymes in the nogalamycin biosynthetic pathway.,Siitonen V, Selvaraj B, Niiranen L, Lindqvist Y, Schneider G, Metsa-Ketela M Proc Natl Acad Sci U S A. 2016 May 10;113(19):5251-6. doi:, 10.1073/pnas.1525034113. Epub 2016 Apr 25. PMID:27114534[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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