2np9

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[[Image:2np9.png|left|200px]]
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==Crystal structure of a dioxygenase in the Crotonase superfamily==
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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 [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2NP9 FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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><br>
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<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DpgC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=55952 Streptomyces toyocaensis])</td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2np9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2np9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2np9 RCSB], [http://www.ebi.ac.uk/pdbsum/2np9 PDBsum]</span></td></tr>
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<table>
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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/chain_selection.php?pdb_ID=2ata ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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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{{STRUCTURE_2np9| PDB=2np9 | SCENE= }}
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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:17507985<ref>PMID:17507985</ref>
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===Crystal structure of a dioxygenase in the Crotonase superfamily===
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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{{ABSTRACT_PUBMED_17507985}}
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== References ==
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<references/>
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==About this Structure==
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__TOC__
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[[2np9]] is a 3 chain structure with sequence from [http://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].
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</StructureSection>
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==Reference==
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<ref group="xtra">PMID:017507985</ref><references group="xtra"/>
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[[Category: Streptomyces toyocaensis]]
[[Category: Streptomyces toyocaensis]]
[[Category: Bruner, S D.]]
[[Category: Bruner, S D.]]

Revision as of 18:01, 30 September 2014

Crystal structure of a dioxygenase in the Crotonase superfamily

2np9, resolution 2.45Å

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