2np9

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(New page: 200px<br /><applet load="2np9" size="350" color="white" frame="true" align="right" spinBox="true" caption="2np9, resolution 2.45&Aring;" /> '''Crystal structure of...)
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[[Image:2np9.jpg|left|200px]]<br /><applet load="2np9" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2np9, resolution 2.45&Aring;" />
 
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'''Crystal structure of a dioxygenase in the Crotonase superfamily'''<br />
 
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==Overview==
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==Crystal structure of a dioxygenase in the Crotonase superfamily==
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Enzyme-catalysed oxidations are some of the most common transformations in, primary and secondary metabolism. The vancomycin biosynthetic enzyme DpgC, belongs to a small class of oxygenation enzymes that are not dependent on, an accessory cofactor or metal ion. The detailed mechanism of, cofactor-independent oxygenases has not been established. Here we report, the first structure of an enzyme of this oxygenase class in complex with a, bound substrate mimic. The use of a designed, synthetic substrate analogue, allows unique insights into the chemistry of oxygen activation. The, structure confirms the absence of cofactors, and electron density, consistent with molecular oxygen is present adjacent to the site of, oxidation on the substrate. Molecular oxygen is bound in a small, hydrophobic pocket and the substrate provides the reducing power to, activate oxygen for downstream chemical steps. Our results resolve the, unique and complex chemistry of DpgC, a key enzyme in the biosynthetic, pathway of an important class of antibiotics. Furthermore, mechanistic, parallels exist between DpgC and cofactor-dependent flavoenzymes, providing information regarding the general mechanism of enzymatic oxygen, activation.
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<StructureSection load='2np9' size='340' side='right'caption='[[2np9]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2np9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_toyocaensis Streptomyces toyocaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NP9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NP9 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.45&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=YE1:[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL+(3R)-4-({3-[(2-{[(3,5-DIHYDROXYPHENYL)ACETYL]AMINO}ETHYL)AMINO]-3-OXOPROPYL}AMINO)-3-HYDROXY-2,2-DIMETHYL-4-OXOBUTYL+DIHYDROGEN+DIPHOSPHATE'>YE1</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2np9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2np9 OCA], [https://pdbe.org/2np9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2np9 RCSB], [https://www.ebi.ac.uk/pdbsum/2np9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2np9 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPGC_STRTO DPGC_STRTO] Involved in the biosynthesis of the nonproteinogenic amino acid monomer (S)-3,5-dihydroxyphenylglycine (Dpg) responsible of the production of vancomycin and teicoplanin antibiotics. Catalyzes the unusual conversion 3,5-dihydroxyphenylacetyl-CoA (DPA-CoA) to 3,5-dihydroxyphenylglyoxylate. DpgC performed a net four-electron oxidation of the benzylic carbon of DPA-CoA and the hydrolysis of the thioester bond to generate free CoA (PubMed:18004875, PubMed:17507985). DpgC has the ability to process a diverse range of substituted phenylacetyl-CoA substrates (PubMed:18004875).<ref>PMID:17507985</ref> <ref>PMID:18004875</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/np/2np9_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2np9 ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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2NP9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_toyocaensis Streptomyces toyocaensis] with <scene name='pdbligand=YE1:'>YE1</scene> and <scene name='pdbligand=OXY:'>OXY</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NP9 OCA].
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*[[Dioxygenase 3D structures|Dioxygenase 3D structures]]
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== References ==
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==Reference==
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<references/>
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Structural basis for cofactor-independent dioxygenation in vancomycin biosynthesis., Widboom PF, Fielding EN, Liu Y, Bruner SD, Nature. 2007 May 17;447(7142):342-5. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17507985 17507985]
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__TOC__
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[[Category: Single protein]]
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Streptomyces toyocaensis]]
[[Category: Streptomyces toyocaensis]]
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[[Category: Bruner, S.D.]]
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[[Category: Bruner SD]]
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[[Category: Fielding, E.N.]]
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[[Category: Fielding EN]]
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[[Category: Widboom, P.F.]]
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[[Category: Widboom PF]]
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[[Category: OXY]]
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[[Category: YE1]]
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[[Category: protein inhibitor complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 14:58:28 2008''
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Current revision

Crystal structure of a dioxygenase in the Crotonase superfamily

PDB ID 2np9

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