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6j24

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Crystal structure of a SAM-dependent methyltransferase LepI in complex with its substrate

Structural highlights

6j24 is a 2 chain structure with sequence from Aspergillus flavus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.244Å
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

S-adenosyl-1-methionine (SAM)-dependent enzymes regulate various disease-related behaviors in all organisms. Recently, the leporin biosynthesis enzyme LepI, a SAM-dependent enzyme, was reported to catalyze pericyclic reactions in leporin biosynthesis; however, the mechanisms underlying LepI activation and catalysis remain unclear. This study aimed to investigate the molecular mechanisms of LepI. Here, we reported crystal structures of LepI bound to SAM/5'-deoxy-5'-(methylthio) adenosine (MTA), S-adenosyl-homocysteine (SAH), and SAM/substrate states. Structural and biochemical analysis revealed that MTA or SAH inhibited the enzyme activities, whereas SAM activated the enzyme. The analysis of the substrate-bound structure of LepI demonstrated that this enzymatic retro-Claisen rearrangement was primarily driven by three critical polar residues His133, Arg197, Arg295 around the active site and assisted by SAM with unclear mechanism. The present studies indicate that the unique mechanisms underlying regulatory and catalysis of the unusual SAM-dependent enzyme LepI, not only strengthening current understanding of the fundamentally biochemical catalysis, but also providing novel insights into the design of SAM-dependent enzyme-specific small molecules.

Deciphering the regulatory and catalytic mechanisms of an unusual SAM-dependent enzyme.,Sun Q, Hu Y, Gu Y, Huang J, He J, Luo L, Yang Y, Yin S, Dou C, Wang T, Fu X, He L, Qi S, Zhu X, Yang S, Wei X, Cheng W Signal Transduct Target Ther. 2019 May 24;4:17. doi: 10.1038/s41392-019-0052-y., eCollection 2019. PMID:31149354^[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
↑ Sun Q, Hu Y, Gu Y, Huang J, He J, Luo L, Yang Y, Yin S, Dou C, Wang T, Fu X, He L, Qi S, Zhu X, Yang S, Wei X, Cheng W. Deciphering the regulatory and catalytic mechanisms of an unusual SAM-dependent enzyme. Signal Transduct Target Ther. 2019 May 24;4:17. doi: 10.1038/s41392-019-0052-y., eCollection 2019. PMID:31149354 doi:http://dx.doi.org/10.1038/s41392-019-0052-y

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/6j24"

Categories: Aspergillus flavus | Large Structures | Qiu S | Wei C

@@ Line 3: / Line 3: @@
 <StructureSection load='6j24' size='340' side='right'caption='[[6j24]], [[Resolution|resolution]] 2.24&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6j24]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aspfl Aspfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J24 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6J24 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6j24]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_flavus Aspergillus flavus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6J24 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6J24 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BYO:(3~{S},4~{R},4~{a}~{S},6~{R},8~{a}~{S})-4,6-dimethyl-5-phenyl-spiro[1~{H}-pyridine-3,5-2,3,4,4~{a},6,8~{a}-hexahydro-1~{H}-naphthalene]-2,4-dione'>BYO</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]] 2.244&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">COH21_002903 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5059 ASPFL])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BYO:(3~{S},4~{R},4~{a}~{S},6~{R},8~{a}~{S})-4,6-dimethyl-5-phenyl-spiro[1~{H}-pyridine-3,5-2,3,4,4~{a},6,8~{a}-hexahydro-1~{H}-naphthalene]-2,4-dione'>BYO</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=6j24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j24 OCA], [http://pdbe.org/6j24 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6j24 RCSB], [http://www.ebi.ac.uk/pdbsum/6j24 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6j24 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=6j24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6j24 OCA], [https://pdbe.org/6j24 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6j24 RCSB], [https://www.ebi.ac.uk/pdbsum/6j24 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6j24 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[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 21: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Aspfl]]
+[[Category: Aspergillus flavus]]
 [[Category: Large Structures]]
-[[Category: Qiu, S]]
+[[Category: Qiu S]]
-[[Category: Wei, C]]
+[[Category: Wei C]]
-[[Category: Complex]]
-[[Category: Transferase]]

6j24

From Proteopedia

Current revision

Crystal structure of a SAM-dependent methyltransferase LepI in complex with its substrate

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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