1pby: Difference between revisions
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==Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from Paracoccus denitrificans at 1.7 A Resolution== | |||
<StructureSection load='1pby' size='340' side='right'caption='[[1pby]], [[Resolution|resolution]] 1.70Å' scene=''> | |||
== Structural highlights == | |||
<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> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</td></tr> | |||
<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> | |||
<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> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q8VUT0_PARDE Q8VUT0_PARDE] | |||
== 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/pb/1pby_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/main_output.php?pdb_ID=1pby ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1pby" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
== | __TOC__ | ||
< | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Paracoccus denitrificans]] | [[Category: Paracoccus denitrificans]] | ||
[[Category: Datta | [[Category: Datta S]] | ||
[[Category: Ikeda | [[Category: Ikeda T]] | ||
[[Category: Kano | [[Category: Kano K]] | ||
[[Category: Mathews | [[Category: Mathews FS]] | ||
Latest revision as of 12:41, 16 August 2023
Structure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from Paracoccus denitrificans at 1.7 A ResolutionStructure of the Phenylhydrazine Adduct of the Quinohemoprotein Amine Dehydrogenase from Paracoccus denitrificans at 1.7 A Resolution
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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