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2vz7

From Proteopedia

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Crystal structure of the YC-17-bound PikC D50N mutant

Structural highlights

2vz7 is a 2 chain structure with sequence from Streptomyces venezuelae. This structure supersedes the now removed PDB entry 2vsj. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.2Å
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

The cytochrome P-450 PikC from Streptomyces venezuelae exhibits significant substrate tolerance and performs multiple hydroxylation reactions on structurally variant macrolides bearing the deoxyamino sugar desosamine. In previously determined co-crystal structures (Sherman, D. H., Li, S., Yermalitskaya, L. V., Kim, Y., Smith, J. A., Waterman, M. R., and Podust, L. M. (2006) J. Biol. Chem. 281, 26289-26297), the desosamine moiety of the native substrates YC-17 and narbomycin is bound in two distinct buried and surface-exposed binding pockets, mediated by specific interactions between the protonated dimethylamino group and the acidic amino acid residues Asp(50), Glu(85), and Glu(94). Although the Glu(85) and Glu(94) negative charges are essential for maximal catalytic activity of native enzyme, elimination of the surface-exposed negative charge at Asp(50) results in significantly enhanced catalytic activity. Nevertheless, the D50N substitution could not rescue catalytic activity of PikC(E94Q) based on lack of activity in the corresponding double mutant PikC(D50N/E94Q). To address the specific role for each desosamine-binding pocket, we analyzed the x-ray structures of the PikC(D50N) mutant co-crystallized with narbomycin (1.85A resolution) and YC-17 (3.2A resolution). In PikC(D50N), the desosamine moiety of both YC-17 and narbomycin was bound in a catalytically productive "buried site." This finding suggested a two-step substrate binding mechanism, whereby desosamine is recognized in the two subsites to allow the macrolide substrate to sequentially progress toward a catalytically favorable orientation. Collectively, the binding, mutagenesis, kinetic, and x-ray structural data suggest that enhancement of the catalytic activity of PikC(D50N) is due to the facilitated relocation of substrate to the buried site, which has higher binding affinity, as opposed to dissociation in solution from the transient "surface-exposed site."

Analysis of transient and catalytic desosamine-binding pockets in cytochrome P-450 PikC from Streptomyces venezuelae.,Li S, Ouellet H, Sherman DH, Podust LM J Biol Chem. 2009 Feb 27;284(9):5723-30. Epub 2009 Jan 4. PMID:19124459^[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, 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

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/2vz7"

Categories: Large Structures | Streptomyces venezuelae | Li S | Podust LM | Sherman DH

@@ Line 1: / Line 1: @@
-==CRYSTAL STRUCTURE OF THE YC-17-BOUND PIKC D50N MUTANT==
-<StructureSection load='2vz7' size='340' side='right' caption='[[2vz7]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+==Crystal structure of the YC-17-bound PikC D50N mutant==
+<StructureSection load='2vz7' size='340' side='right'caption='[[2vz7]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vz7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_venezuelae Streptomyces venezuelae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vsj 2vsj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VZ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VZ7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2vz7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_venezuelae Streptomyces venezuelae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2vsj 2vsj]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VZ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VZ7 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PXI:4-{[4-(DIMETHYLAMINO)-3-HYDROXY-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL]OXY}-12-ETHYL-3,5,7,11-TETRAMETHYLOXACYCLODODEC-9-ENE-2,8-DIONE'>PXI</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]] 3.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2cd8|2cd8]], [[2ca0|2ca0]], [[2c6h|2c6h]], [[2bvj|2bvj]], [[2c7x|2c7x]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PXI:4-{[4-(DIMETHYLAMINO)-3-HYDROXY-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL]OXY}-12-ETHYL-3,5,7,11-TETRAMETHYLOXACYCLODODEC-9-ENE-2,8-DIONE'>PXI</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=2vz7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vz7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vz7 RCSB], [http://www.ebi.ac.uk/pdbsum/2vz7 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=2vz7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vz7 OCA], [https://pdbe.org/2vz7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vz7 RCSB], [https://www.ebi.ac.uk/pdbsum/2vz7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vz7 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/vz/2vz7_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vz/2vz7_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vz7 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2vz7" style="background-color:#fffaf0;"></div>
 ==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: Large Structures]]
 [[Category: Streptomyces venezuelae]]
-[[Category: Li, S]]
+[[Category: Li S]]
-[[Category: Podust, L M]]
+[[Category: Podust LM]]
-[[Category: Sherman, D H]]
+[[Category: Sherman DH]]
-[[Category: Antibiotic biosynthesis]]
-[[Category: Cyp107l1]]
-[[Category: Cytochrome p450]]
-[[Category: Heme]]
-[[Category: Iron]]
-[[Category: Macrolide monooxygenase]]
-[[Category: Metal-binding]]
-[[Category: Monooxygenase]]
-[[Category: Oxidoreductase]]
-[[Category: Pikc]]

2vz7

From Proteopedia

Current revision

Crystal structure of the YC-17-bound PikC D50N mutant

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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