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| | <StructureSection load='1rky' size='340' side='right'caption='[[1rky]], [[Resolution|resolution]] 1.68Å' scene=''> | | <StructureSection load='1rky' size='340' side='right'caption='[[1rky]], [[Resolution|resolution]] 1.68Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1rky]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_28485 Atcc 28485]. 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 [http://proteopedia.org/fgij/fg.htm?mol=1RKY FirstGlance]. <br> | + | <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> |
| - | </td></tr><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=XE:XENON'>XE</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.68Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TPQ:5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE'>TPQ</scene></td></tr>
| + | <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> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1n9e|1n9e]], [[1rjo|1rjo]]</div></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=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> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ATCC 28, 485 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4922 ATCC 28485])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1rky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rky OCA], [http://pdbe.org/1rky PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rky RCSB], [http://www.ebi.ac.uk/pdbsum/1rky PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rky ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q96X16_PICPA Q96X16_PICPA] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 28485]] | + | [[Category: Komagataella pastoris]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Protein-lysine 6-oxidase]]
| + | [[Category: Duff AP]] |
| - | [[Category: Duff, A P]] | + | [[Category: Guss JM]] |
| - | [[Category: Guss, J M]] | + | |
| - | [[Category: Amine oxidase]]
| + | |
| - | [[Category: Cao]]
| + | |
| - | [[Category: Copper-containing]]
| + | |
| - | [[Category: Cuao]]
| + | |
| - | [[Category: Dioxygen binding site]]
| + | |
| - | [[Category: Lysyl oxidase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Oxygen binding site]]
| + | |
| - | [[Category: Pplo]]
| + | |
| - | [[Category: Quinone]]
| + | |
| - | [[Category: Tpq]]
| + | |
| - | [[Category: Trihydroxyphenylalanine quinone]]
| + | |
| - | [[Category: Xenon]]
| + | |
| Structural highlights
1rky is a 1 chain structure with sequence from Komagataella pastoris. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.68Å |
| Ligands: | , , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
Q96X16_PICPA
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Duff AP, Trambaiolo DM, Cohen AE, Ellis PJ, Juda GA, Shepard EM, Langley DB, Dooley DM, Freeman HC, Guss JM. Using xenon as a probe for dioxygen-binding sites in copper amine oxidases. J Mol Biol. 2004 Nov 26;344(3):599-607. PMID:15533431 doi:10.1016/j.jmb.2004.09.075
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