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2ygx

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Structure of the mixed-function P450 MycG in P21 space group

Structural highlights

2ygx is a 4 chain structure with sequence from Micromonospora griseorubida. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.39Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MYCG_MICGR Involved in the biosynthesis of mycinamicin, a 16-membered macrolide antibiotic. Catalyzes consecutive hydroxylation (at C14) and epoxidation (at C12-C13) reactions with mycinamicin IV as initial substrate, leading to mycinamicin II. These reactions require prior dimethylation of 6-deoxyallose to mycinose for effective conversion by the dual function MycG enzyme.^[1] ^[2] ^[3]

Publication Abstract from PubMed

The majority of characterized cytochrome P450 enzymes in actinomycete secondary metabolic pathways are strictly substrate-, regio- and stereo-specific. Examples of multifunctional biosynthetic cytochromes P450 with broader substrate and regio-specificity are growing in number and are of particular interest for biosynthetic and chemoenzymatic applications. MycG is among the first P450 monooxygenases characterized that catalyzes both hydroxylation and epoxidation reactions in the final biosynthetic steps, leading to oxidative tailoring of the 16-membered ring macrolide antibiotic mycinamicin II (M-II) in the actinomycete Micromonospora griseorubida. The ordering of steps to complete the biosynthetic process involves a complex substrate recognition pattern by the enzyme and interplay between three tailoring modifications: glycosylation, methylation and oxidation. To understand the catalytic properties of MycG, we structurally characterized the ligand-free enzyme and its complexes with three native metabolites. These include substrates mycinamicin IV (M-IV) and V (M-V), and their biosynthetic precursor mycinamicin III (M-III), which carries the monomethoxy sugar javose instead of the dimethoxylated sugar mycinose. The two methoxy groups of mycinose serve as sensors that mediate initial recognition to discriminate between closely related substrates in the post-polyketide oxidative tailoring of mycinamycin metabolites. Since x-ray structures alone did not explain the mechanisms of macrolide hydroxylation and epoxidation, paramagnetic NMR relaxation measurements were conducted. Molecular modeling based on these data indicates that in solution substrate may penetrate the active site sufficiently to place the abstracted hydrogen atom of M-IV within 6 A of the heme iron, and ~4 A of the oxygen of Fe-ligated water.

Substrate recognition by the multifunctional cytochrome P450 MycG in mycinamicin hydroxylation and epoxidation reactions.,Li S, Tietz DR, Rutaganira FU, Kells PM, Anzai Y, Kato F, Pochapsky TC, Sherman DH, Podust LM J Biol Chem. 2012 Sep 5. PMID:22952225^[4]

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

References

↑ Anzai Y, Li S, Chaulagain MR, Kinoshita K, Kato F, Montgomery J, Sherman DH. Functional analysis of MycCI and MycG, cytochrome P450 enzymes involved in biosynthesis of mycinamicin macrolide antibiotics. Chem Biol. 2008 Sep 22;15(9):950-9. doi: 10.1016/j.chembiol.2008.07.014. PMID:18804032 doi:http://dx.doi.org/10.1016/j.chembiol.2008.07.014
↑ Anzai Y, Tsukada S, Sakai A, Masuda R, Harada C, Domeki A, Li S, Kinoshita K, Sherman DH, Kato F. Function of cytochrome P450 enzymes MycCI and MycG in Micromonospora griseorubida, a producer of the macrolide antibiotic mycinamicin. Antimicrob Agents Chemother. 2012 Jul;56(7):3648-56. doi: 10.1128/AAC.06063-11., Epub 2012 Apr 30. PMID:22547618 doi:http://dx.doi.org/10.1128/AAC.06063-11
↑ Inouye M, Takada Y, Muto N, Beppu T, Horinouchi S. Characterization and expression of a P-450-like mycinamicin biosynthesis gene using a novel Micromonospora-Escherichia coli shuttle cosmid vector. Mol Gen Genet. 1994 Nov 15;245(4):456-64. PMID:7808395
↑ Li S, Tietz DR, Rutaganira FU, Kells PM, Anzai Y, Kato F, Pochapsky TC, Sherman DH, Podust LM. Substrate recognition by the multifunctional cytochrome P450 MycG in mycinamicin hydroxylation and epoxidation reactions. J Biol Chem. 2012 Sep 5. PMID:22952225 doi:http://dx.doi.org/10.1074/jbc.M112.410340

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/2ygx"

@@ Line 3: / Line 3: @@
 <StructureSection load='2ygx' size='340' side='right'caption='[[2ygx]], [[Resolution|resolution]] 2.39&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ygx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/'micromonospora_griseorubida' 'micromonospora griseorubida']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YGX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YGX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ygx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Micromonospora_griseorubida Micromonospora griseorubida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YGX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YGX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 2.39&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2y5n|2y5n]], [[2yca|2yca]], [[2y46|2y46]], [[2y5z|2y5z]], [[2y98|2y98]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=2ygx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ygx OCA], [https://pdbe.org/2ygx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ygx RCSB], [https://www.ebi.ac.uk/pdbsum/2ygx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ygx ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/MYCG_MICGR MYCG_MICGR] Involved in the biosynthesis of mycinamicin, a 16-membered macrolide antibiotic. Catalyzes consecutive hydroxylation (at C14) and epoxidation (at C12-C13) reactions with mycinamicin IV as initial substrate, leading to mycinamicin II. These reactions require prior dimethylation of 6-deoxyallose to mycinose for effective conversion by the dual function MycG enzyme.<ref>PMID:18804032</ref> <ref>PMID:22547618</ref> <ref>PMID:7808395</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Micromonospora griseorubida]]
 [[Category: Large Structures]]
-[[Category: Kells, P M]]
+[[Category: Micromonospora griseorubida]]
-[[Category: Li, S]]
+[[Category: Kells PM]]
-[[Category: Podust, L M]]
+[[Category: Li S]]
-[[Category: Rutaganira, F U]]
+[[Category: Podust LM]]
-[[Category: Sherman, D H]]
+[[Category: Rutaganira FU]]
-[[Category: Electron transport]]
+[[Category: Sherman DH]]
-[[Category: Metal binding]]
-[[Category: Mycinamicin biosynthesis]]

2ygx

From Proteopedia

Current revision

Structure of the mixed-function P450 MycG in P21 space group

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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