1rky

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[[Image:1rky.gif|left|200px]]
 
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{{Structure
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==PPLO + Xe==
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|PDB= 1rky |SIZE=350|CAPTION= <scene name='initialview01'>1rky</scene>, resolution 1.68&Aring;
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<StructureSection load='1rky' size='340' side='right'caption='[[1rky]], [[Resolution|resolution]] 1.68&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene> and <scene name='pdbligand=XE:XENON'>XE</scene>
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<table><tr><td colspan='2'>[[1rky]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Komagataella_pastoris Komagataella pastoris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RKY FirstGlance]. <br>
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|ACTIVITY= [http://en.wikipedia.org/wiki/Protein-lysine_6-oxidase Protein-lysine 6-oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.13 1.4.3.13]
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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]] 1.68&#8491;</td></tr>
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|GENE= ATCC 28, 485 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4922 Pichia pastoris])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=TPQ:5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE'>TPQ</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr>
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}}
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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=1rky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rky OCA], [https://pdbe.org/1rky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rky RCSB], [https://www.ebi.ac.uk/pdbsum/1rky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rky ProSAT]</span></td></tr>
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</table>
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'''PPLO + Xe'''
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== Function ==
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[https://www.uniprot.org/uniprot/Q96X16_PICPA Q96X16_PICPA]
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== Evolutionary Conservation ==
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==Overview==
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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/rk/1rky_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=1rky 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 ==
Potential dioxygen-binding sites in three Cu amine oxidases have been investigated by recording X-ray diffraction data at 1.7-2.2A resolution for crystals under a high pressure of xenon gas. Electron-density difference maps and crystallographic refinement provide unequivocal evidence for a number of Xe-binding sites in each enzyme. Only one of these sites is present in all three Cu amine oxidases studied. Structural changes elsewhere in the protein molecules are insignificant. The results illustrate the use of xenon as a probe for cavities, in which a protein may accommodate a dioxygen molecule. The finding of a potential dioxygen-binding cavity close to the active site of Cu amine oxidases may be relevant to the function of the enzymes, since the formation of a transient protein-dioxygen complex is a likely step in the catalytic mechanism. No evidence was found for xenon binding in a region of the molecule that was previously identified in two other Cu amine oxidases as a potential transient dioxygen-binding site.
Potential dioxygen-binding sites in three Cu amine oxidases have been investigated by recording X-ray diffraction data at 1.7-2.2A resolution for crystals under a high pressure of xenon gas. Electron-density difference maps and crystallographic refinement provide unequivocal evidence for a number of Xe-binding sites in each enzyme. Only one of these sites is present in all three Cu amine oxidases studied. Structural changes elsewhere in the protein molecules are insignificant. The results illustrate the use of xenon as a probe for cavities, in which a protein may accommodate a dioxygen molecule. The finding of a potential dioxygen-binding cavity close to the active site of Cu amine oxidases may be relevant to the function of the enzymes, since the formation of a transient protein-dioxygen complex is a likely step in the catalytic mechanism. No evidence was found for xenon binding in a region of the molecule that was previously identified in two other Cu amine oxidases as a potential transient dioxygen-binding site.
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==About this Structure==
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Using xenon as a probe for dioxygen-binding sites in copper amine oxidases.,Duff AP, Trambaiolo DM, Cohen AE, Ellis PJ, Juda GA, Shepard EM, Langley DB, Dooley DM, Freeman HC, Guss JM J Mol Biol. 2004 Nov 26;344(3):599-607. PMID:15533431<ref>PMID:15533431</ref>
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1RKY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pichia_pastoris Pichia pastoris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RKY OCA].
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==Reference==
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Using xenon as a probe for dioxygen-binding sites in copper amine oxidases., Duff AP, Trambaiolo DM, Cohen AE, Ellis PJ, Juda GA, Shepard EM, Langley DB, Dooley DM, Freeman HC, Guss JM, J Mol Biol. 2004 Nov 26;344(3):599-607. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15533431 15533431]
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[[Category: Pichia pastoris]]
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[[Category: Protein-lysine 6-oxidase]]
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[[Category: Single protein]]
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[[Category: Duff, A P.]]
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[[Category: Guss, J M.]]
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[[Category: CA]]
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[[Category: CL]]
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[[Category: CU]]
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[[Category: IMD]]
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[[Category: MG]]
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[[Category: NAG]]
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[[Category: XE]]
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[[Category: amine oxidase]]
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[[Category: cao]]
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[[Category: copper-containing]]
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[[Category: cuao]]
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[[Category: dioxygen binding site]]
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[[Category: lysyl oxidase]]
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[[Category: oxygen binding site]]
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[[Category: pplo]]
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[[Category: quinone]]
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[[Category: tpq]]
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[[Category: trihydroxyphenylalanine quinone]]
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[[Category: xenon]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:53:03 2008''
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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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<div class="pdbe-citations 1rky" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Komagataella pastoris]]
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[[Category: Large Structures]]
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[[Category: Duff AP]]
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[[Category: Guss JM]]

Current revision

PPLO + Xe

PDB ID 1rky

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