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1pby

From Proteopedia

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{{Seed}}
 
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[[Image:1pby.png|left|200px]]
 
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==Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from Paracoccus denitrificans at 1.7 A Resolution==
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The line below this paragraph, containing "STRUCTURE_1pby", creates the "Structure Box" on the page.
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<StructureSection load='1pby' size='340' side='right'caption='[[1pby]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1pby]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PBY FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.7&#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=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=TBU:TERTIARY-BUTYL+ALCOHOL'>TBU</scene>, <scene name='pdbligand=TRW:TRW3-(2-AMINO-3-HYDROXY-PROPYL)-6-(N-CYCLOHEXYL-HYDRAZINO)OCTAHYDRO-INDOL-7-OL'>TRW</scene></td></tr>
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{{STRUCTURE_1pby| PDB=1pby | SCENE= }}
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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=1pby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pby OCA], [https://pdbe.org/1pby PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pby RCSB], [https://www.ebi.ac.uk/pdbsum/1pby PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pby ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q8VUT0_PARDE Q8VUT0_PARDE]
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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/pb/1pby_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=1pby 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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The 109 kDa quinohemoprotein amine dehydrogenase (QHNDH) from Paracoccus denitrificans contains a novel redox cofactor, cysteine tryptophylquinone (CTQ). This cofactor is derived from a pair of gene-encoded amino acids by post-translational modification and was previously identified and characterized within an 82-residue subunit by chemical methods and crystallographic analysis at 2.05 A resolution. It contains an orthoquinone moiety bound to the indole ring and catalyzes the oxidation of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms. This paper reports the structural analysis of the complex of QHNDH with the enzyme inhibitor phenylhydrazine determined at 1.70 A resolution. The phenylhydrazone product is attached to the C6 position, identifying the O6 atom of CTQ as the site of Schiff-base formation as postulated by analogy to another amine-oxidizing enzyme, methylamine dehydrogenase. Furthermore, the inner N atom closest to the phenyl ring of phenylhydrazine forms a hydrogen bond to gammaAsp33 in the complex, lending support to the hypothesis that this residue serves as the active-site base for proton abstraction during catalysis.
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===Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from Paracoccus denitrificans at 1.7 A Resolution===
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Structure of the phenylhydrazine adduct of the quinohemoprotein amine dehydrogenase from Paracoccus denitrificans at 1.7 A resolution.,Datta S, Ikeda T, Kano K, Mathews FS Acta Crystallogr D Biol Crystallogr. 2003 Sep;59(Pt 9):1551-6. Epub 2003, Aug 19. PMID:12925784<ref>PMID:12925784</ref>
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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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The line below this paragraph, {{ABSTRACT_PUBMED_12925784}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1pby" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 12925784 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_12925784}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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1PBY is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PBY OCA].
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==Reference==
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<ref group="xtra">PMID:12925784</ref><references group="xtra"/>
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[[Category: Amine dehydrogenase]]
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[[Category: Paracoccus denitrificans]]
[[Category: Paracoccus denitrificans]]
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[[Category: Datta, S.]]
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[[Category: Datta S]]
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[[Category: Ikeda, T.]]
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[[Category: Ikeda T]]
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[[Category: Kano, K.]]
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[[Category: Kano K]]
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[[Category: Mathews, F S.]]
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[[Category: Mathews FS]]
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[[Category: Amine dehydrogenase]]
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[[Category: Quinohemoprotein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:02:01 2009''
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Current revision

Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from Paracoccus denitrificans at 1.7 A Resolution

PDB ID 1pby

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