6ix5

From Proteopedia

(Difference between revisions)

Current revision

The structure of LepI complex with SAM and its substrate analogue

Structural highlights

6ix5 is a 2 chain structure with sequence from Aspergillus flavus NRRL3357. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.7Å
Ligands:	, , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LEPI_ASPFN O-methyltransferase; part of the gene cluster 23 that mediates the biosynthesis of a family of 2-pyridones known as leporins (PubMed:20447271, PubMed:26051490). The hybrid PKS-NRPS synthetase lepA and the enoyl reductase lepG are responsible for fusion of phenylalanine with a hexaketide and subsequent release of the stable tetramic acid precursor, pre-leporin C (PubMed:26051490). Because lepA lacks a designated enoylreductase (ER) domain, the required activity is provided the enoyl reductase lepG (PubMed:26051490). It is possible that the dehydrogenase lepF also participates in production of pre-leporin C (PubMed:26051490). Cytochrome P450 monooxygenase lepH is then required for the ring expansion step to yield leporin C (PubMed:26051490). Leporin C is then presumably further oxidized by the N-hydroxylase lepD to form leporin B (PubMed:26051490). LepI may possess a function in biosynthesis upstream of lepA (PubMed:26051490). Leporin B is further oxidized in the presence of ferric ion to give the leporin B trimer-iron chelate, but whether or not this reaction is catalyzed by an enzyme in the pathway or by ferric ion is not determined yet (PubMed:26051490).^[1] ^[2]

Publication Abstract from PubMed

LepI is an S-adenosylmethionine (SAM)-dependent pericyclase that catalyses the formation of the 2-pyridone natural product leporin C. Biochemical characterization has shown that LepI can catalyse stereoselective dehydration to yield a reactive (E)-quinone methide that can undergo bifurcating intramolecular Diels-Alder (IMDA) and hetero-Diels-Alder (HDA) cyclizations from an ambimodal transition state, as well as a [3,3]-retro-Claisen rearrangement to recycle the IMDA product into leporin C. Here, we solve the X-ray crystal structures of SAM-bound LepI and in complex with a substrate analogue, the product leporin C, and a retro-Claisen reaction transition-state analogue to understand the structural basis for the multitude of reactions. Structural and mutational analysis reveals how nature evolves a classic methyltransferase active site into one that can serve as a dehydratase and a multifunctional pericyclase. Catalysis of both sets of reactions employs H133 and R295, two active-site residues that are not found in canonical methyltransferases. An alternative role of SAM, which is not found to be in direct contact with the substrate, is also proposed.

Structural basis for stereoselective dehydration and hydrogen-bonding catalysis by the SAM-dependent pericyclase LepI.,Cai Y, Hai Y, Ohashi M, Jamieson CS, Garcia-Borras M, Houk KN, Zhou J, Tang Y Nat Chem. 2019 Jul 22. pii: 10.1038/s41557-019-0294-x. doi:, 10.1038/s41557-019-0294-x. PMID:31332284^[3]

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

References

↑ Cary JW, Uka V, Han Z, Buyst D, Harris-Coward PY, Ehrlich KC, Wei Q, Bhatnagar D, Dowd PF, Martens SL, Calvo AM, Martins JC, Vanhaecke L, Coenye T, De Saeger S, Di Mavungu JD. An Aspergillus flavus secondary metabolic gene cluster containing a hybrid PKS-NRPS is necessary for synthesis of the 2-pyridones, leporins. Fungal Genet Biol. 2015 Aug;81:88-97. doi: 10.1016/j.fgb.2015.05.010. Epub 2015, Jun 4. PMID:26051490 doi:http://dx.doi.org/10.1016/j.fgb.2015.05.010
↑ Georgianna DR, Fedorova ND, Burroughs JL, Dolezal AL, Bok JW, Horowitz-Brown S, Woloshuk CP, Yu J, Keller NP, Payne GA. Beyond aflatoxin: four distinct expression patterns and functional roles associated with Aspergillus flavus secondary metabolism gene clusters. Mol Plant Pathol. 2010 Mar;11(2):213-26. doi: 10.1111/j.1364-3703.2009.00594.x. PMID:20447271 doi:http://dx.doi.org/10.1111/j.1364-3703.2009.00594.x
↑ Cai Y, Hai Y, Ohashi M, Jamieson CS, Garcia-Borras M, Houk KN, Zhou J, Tang Y. Structural basis for stereoselective dehydration and hydrogen-bonding catalysis by the SAM-dependent pericyclase LepI. Nat Chem. 2019 Jul 22. pii: 10.1038/s41557-019-0294-x. doi:, 10.1038/s41557-019-0294-x. PMID:31332284 doi:http://dx.doi.org/10.1038/s41557-019-0294-x

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6ix5"

@@ Line 3: / Line 3: @@
 <StructureSection load='6ix5' size='340' side='right'caption='[[6ix5]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ix5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspfn Aspfn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IX5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IX5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ix5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_flavus_NRRL3357 Aspergillus flavus NRRL3357]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IX5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IX5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B0L:4-hydroxy-3-[(2S,6E,8E)-2-methyldeca-6,8-dienoyl]-5-phenylpyridin-2(1H)-one'>B0L</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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]] 1.7&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lepI, AFLA_066940 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=332952 ASPFN])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B0L:4-hydroxy-3-[(2S,6E,8E)-2-methyldeca-6,8-dienoyl]-5-phenylpyridin-2(1H)-one'>B0L</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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=6ix5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ix5 OCA], [http://pdbe.org/6ix5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ix5 RCSB], [http://www.ebi.ac.uk/pdbsum/6ix5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ix5 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=6ix5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ix5 OCA], [https://pdbe.org/6ix5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ix5 RCSB], [https://www.ebi.ac.uk/pdbsum/6ix5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ix5 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/LEPI_ASPFN LEPI_ASPFN]] O-methyltransferase; part of the gene cluster 23 that mediates the biosynthesis of a family of 2-pyridones known as leporins (PubMed:20447271, PubMed:26051490). The hybrid PKS-NRPS synthetase lepA and the enoyl reductase lepG are responsible for fusion of phenylalanine with a hexaketide and subsequent release of the stable tetramic acid precursor, pre-leporin C (PubMed:26051490). Because lepA lacks a designated enoylreductase (ER) domain, the required activity is provided the enoyl reductase lepG (PubMed:26051490). It is possible that the dehydrogenase lepF also participates in production of pre-leporin C (PubMed:26051490). Cytochrome P450 monooxygenase lepH is then required for the ring expansion step to yield leporin C (PubMed:26051490). Leporin C is then presumably further oxidized by the N-hydroxylase lepD to form leporin B (PubMed:26051490). LepI may possess a function in biosynthesis upstream of lepA (PubMed:26051490). Leporin B is further oxidized in the presence of ferric ion to give the leporin B trimer-iron chelate, but whether or not this reaction is catalyzed by an enzyme in the pathway or by ferric ion is not determined yet (PubMed:26051490).<ref>PMID:26051490</ref> <ref>PMID:20447271</ref>
+[https://www.uniprot.org/uniprot/LEPI_ASPFN LEPI_ASPFN] O-methyltransferase; part of the gene cluster 23 that mediates the biosynthesis of a family of 2-pyridones known as leporins (PubMed:20447271, PubMed:26051490). The hybrid PKS-NRPS synthetase lepA and the enoyl reductase lepG are responsible for fusion of phenylalanine with a hexaketide and subsequent release of the stable tetramic acid precursor, pre-leporin C (PubMed:26051490). Because lepA lacks a designated enoylreductase (ER) domain, the required activity is provided the enoyl reductase lepG (PubMed:26051490). It is possible that the dehydrogenase lepF also participates in production of pre-leporin C (PubMed:26051490). Cytochrome P450 monooxygenase lepH is then required for the ring expansion step to yield leporin C (PubMed:26051490). Leporin C is then presumably further oxidized by the N-hydroxylase lepD to form leporin B (PubMed:26051490). LepI may possess a function in biosynthesis upstream of lepA (PubMed:26051490). Leporin B is further oxidized in the presence of ferric ion to give the leporin B trimer-iron chelate, but whether or not this reaction is catalyzed by an enzyme in the pathway or by ferric ion is not determined yet (PubMed:26051490).<ref>PMID:26051490</ref> <ref>PMID:20447271</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Aspfn]]
+[[Category: Aspergillus flavus NRRL3357]]
 [[Category: Large Structures]]
-[[Category: Cai, Y]]
+[[Category: Cai Y]]
-[[Category: Hai, Y]]
+[[Category: Hai Y]]
-[[Category: Ohashi, M]]
+[[Category: Ohashi M]]
-[[Category: Tang, Y]]
+[[Category: Tang Y]]
-[[Category: Zhou, J]]
+[[Category: Zhou J]]
-[[Category: Biosynthetic protein]]
-[[Category: Leporin]]
-[[Category: O-methyltransferase]]
-[[Category: Pericyclase]]
-[[Category: Sam]]

6ix5

From Proteopedia

Current revision

The structure of LepI complex with SAM and its substrate analogue

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

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