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2wi9

From Proteopedia

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Selective oxidation of carbolide C-H bonds by engineered macrolide P450 monooxygenase

Structural highlights

2wi9 is a 2 chain structure with sequence from Streptomyces venezuelae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PIKC_STRVZ Catalyzes the hydroxylation of narbomycin to give rise to pikromycin, and of 10-deoxymethymycin (YC-17) to give rise to methymycin and neomethymycin during macrolide antibiotic biosynthesis. In addition, produces low amounts of neopicromycin, novapikromycin and novamethymycin. Requires the participation of a ferredoxin and a ferredoxin reductase for the transfer of electrons from NADPH to the monooxygenase.^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Regio- and stereoselective oxidation of an unactivated C-H bond remains a central challenge in organic chemistry. Considerable effort has been devoted to identifying transition metal complexes, biological catalysts, or simplified mimics, but limited success has been achieved. Cytochrome P450 mono-oxygenases are involved in diverse types of regio- and stereoselective oxidations, and represent a promising biocatalyst to address this challenge. The application of this class of enzymes is particularly significant if their substrate spectra can be broadened, selectivity controlled, and reactions catalyzed in the absence of expensive heterologous redox partners. In this study, we engineered a macrolide biosynthetic P450 mono-oxygenase PikC (PikC(D50N)-RhFRED) with remarkable substrate flexibility, significantly increased activity compared to wild-type enzyme, and self-sufficiency. By harnessing its unique desosamine-anchoring functionality via a heretofore under-explored "substrate engineering" strategy, we demonstrated the ability of PikC to hydroxylate a series of carbocyclic rings linked to the desosamine glycoside via an acetal linkage (referred to as "carbolides") in a regioselective manner. Complementary analysis of a number of high-resolution enzyme-substrate cocrystal structures provided significant insights into the function of the aminosugar-derived anchoring group for control of reaction site selectivity. Moreover, unexpected biological activity of a select number of these carbolide systems revealed their potential as a previously unrecorded class of antibiotics.

Selective oxidation of carbolide C-H bonds by an engineered macrolide P450 mono-oxygenase.,Li S, Chaulagain MR, Knauff AR, Podust LM, Montgomery J, Sherman DH Proc Natl Acad Sci U S A. 2009 Oct 15. PMID:19833867^[7]

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

References

↑ Sherman DH, Li S, Yermalitskaya LV, Kim Y, Smith JA, Waterman MR, Podust LM. The structural basis for substrate anchoring, active site selectivity, and product formation by P450 PikC from Streptomyces venezuelae. J Biol Chem. 2006 Sep 8;281(36):26289-97. Epub 2006 Jul 6. PMID:16825192 doi:10.1074/jbc.M605478200
↑ Li S, Ouellet H, Sherman DH, Podust LM. Analysis of transient and catalytic desosamine-binding pockets in cytochrome P-450 PikC from Streptomyces venezuelae. J Biol Chem. 2009 Feb 27;284(9):5723-30. Epub 2009 Jan 4. PMID:19124459 doi:10.1074/jbc.M807592200
↑ Li S, Chaulagain MR, Knauff AR, Podust LM, Montgomery J, Sherman DH. Selective oxidation of carbolide C-H bonds by an engineered macrolide P450 mono-oxygenase. Proc Natl Acad Sci U S A. 2009 Oct 15. PMID:19833867
↑ Negretti S, Narayan AR, Chiou KC, Kells PM, Stachowski JL, Hansen DA, Podust LM, Montgomery J, Sherman DH. Directing Group-Controlled Regioselectivity in an Enzymatic C-H Bond Oxygenation. J Am Chem Soc. 2014 Mar 21. PMID:24627965 doi:http://dx.doi.org/10.1021/ja5016052
↑ Betlach MC, Kealey JT, Ashley GW, McDaniel R. Characterization of the macrolide P-450 hydroxylase from Streptomyces venezuelae which converts narbomycin to picromycin. Biochemistry. 1998 Oct 20;37(42):14937-42. PMID:9778370 doi:10.1021/bi981699c
↑ Xue Y, Wilson D, Zhao L, Liu Hw, Sherman DH. Hydroxylation of macrolactones YC-17 and narbomycin is mediated by the pikC-encoded cytochrome P450 in Streptomyces venezuelae. Chem Biol. 1998 Nov;5(11):661-7. PMID:9831532 doi:10.1016/s1074-5521(98)90293-9
↑ Li S, Chaulagain MR, Knauff AR, Podust LM, Montgomery J, Sherman DH. Selective oxidation of carbolide C-H bonds by an engineered macrolide P450 mono-oxygenase. Proc Natl Acad Sci U S A. 2009 Oct 15. PMID:19833867

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2wi9"

@@ Line 1: / Line 1: @@
-==SELECTIVE OXIDATION OF CARBOLIDE C-H BONDS BY ENGINEERED MACROLIDE P450 MONOOXYGENASE==
-<StructureSection load='2wi9' size='340' side='right' caption='[[2wi9]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+==Selective oxidation of carbolide C-H bonds by engineered macrolide P450 monooxygenase==
+<StructureSection load='2wi9' size='340' side='right'caption='[[2wi9]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2wi9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/As_4.1526 As 4.1526]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WI9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2WI9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2wi9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_venezuelae Streptomyces venezuelae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WI9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WI9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1D2:CYCLODODECYL+3,4,6-TRIDEOXY-3-(DIMETHYLAMINO)-BETA-D-XYLO-HEXOPYRANOSIDE'>1D2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2cd8|2cd8]], [[2ca0|2ca0]], [[2bvj|2bvj]], [[2c7x|2c7x]], [[2vzm|2vzm]], [[2c6h|2c6h]], [[2vz7|2vz7]], [[2whw|2whw]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1D2:CYCLODODECYL+3,4,6-TRIDEOXY-3-(DIMETHYLAMINO)-BETA-D-XYLO-HEXOPYRANOSIDE'>1D2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=2wi9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wi9 OCA], [http://pdbe.org/2wi9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2wi9 RCSB], [http://www.ebi.ac.uk/pdbsum/2wi9 PDBsum]</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=2wi9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wi9 OCA], [https://pdbe.org/2wi9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wi9 RCSB], [https://www.ebi.ac.uk/pdbsum/2wi9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wi9 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PIKC_STRVZ PIKC_STRVZ] Catalyzes the hydroxylation of narbomycin to give rise to pikromycin, and of 10-deoxymethymycin (YC-17) to give rise to methymycin and neomethymycin during macrolide antibiotic biosynthesis. In addition, produces low amounts of neopicromycin, novapikromycin and novamethymycin. Requires the participation of a ferredoxin and a ferredoxin reductase for the transfer of electrons from NADPH to the monooxygenase.<ref>PMID:16825192</ref> <ref>PMID:19124459</ref> <ref>PMID:19833867</ref> <ref>PMID:24627965</ref> <ref>PMID:9778370</ref> <ref>PMID:9831532</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wi/2wi9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wi/2wi9_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 28: / Line 31: @@
 ==See Also==
-*[[Cytochrome P450|Cytochrome P450]]
+*[[Cytochrome P450 3D structures|Cytochrome P450 3D structures]]
+*[[Cytochrome P450 hydroxylase 3D structures|Cytochrome P450 hydroxylase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: As 4 1526]]
+[[Category: Large Structures]]
-[[Category: Chaulagain, M R]]
+[[Category: Streptomyces venezuelae]]
-[[Category: Knauff, A R]]
+[[Category: Chaulagain MR]]
-[[Category: Li, S]]
+[[Category: Knauff AR]]
-[[Category: Montgomery, J]]
+[[Category: Li S]]
-[[Category: Podust, L M]]
+[[Category: Montgomery J]]
-[[Category: Sherman, D H]]
+[[Category: Podust LM]]
-[[Category: Antibiotic biosynthesis]]
+[[Category: Sherman DH]]
-[[Category: Cyp107l1]]
-[[Category: Cytochrome p450]]
-[[Category: Heme]]
-[[Category: Iron]]
-[[Category: Macrolide monooxygenase]]
-[[Category: Metal-binding]]
-[[Category: Monooxygenase]]
-[[Category: Oxidoreductase]]
-[[Category: Oxidoreductase antibiotic biosynthesis]]
-[[Category: Pikc]]

2wi9

From Proteopedia

Current revision

Selective oxidation of carbolide C-H bonds by engineered macrolide P450 monooxygenase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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