1w7c: Difference between revisions

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-[[Image:1w7c.gif|left|200px]]<br /><applet load="1w7c" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1w7c, resolution 1.23&Aring;" />
-'''PPLO AT 1.23 ANGSTROMS'''<br />
-==Overview==
+==PPLO at 1.23 Angstroms==
-The structure of Pichia pastoris lysyl oxidase (PPLO) in a new crystal, form has been refined at 1.23 Angstrom resolution. PPLO, a copper amine, oxidase (CuAO) with a 2,4,5-trihydroxyphenylalanine quinone (TPQ), cofactor, differs from most other members of the CuAO enzyme family in, having the ability to oxidize the side chain of lysine residues in a, polypeptide. In the asymmetric unit of the crystals, the structure, analysis has located residues 43-779 of the polypeptide chain, seven, carbohydrate residues, the active-site Cu atom, an imidazole molecule, bound at the active site, two buried Ca(2+) ions, five surface Mg(2+), ions, five surface Cl(-) ions and 1045 water molecules. The, crystallographic residuals are R = 0.112 and R(free) = 0.146. The TPQ, cofactor and several other active-site residues are poorly ordered, in, contrast to the surrounding well ordered structure. A covalent cross-link, is observed between two lysine residues, Lys778 and Lys66. The cross-link, is likely to have been formed by the oxidation of Lys778 followed by a, spontaneous reaction with Lys66. The link is modelled as, dehydrolysinonorleucine.
+<StructureSection load='1w7c' size='340' side='right'caption='[[1w7c]], [[Resolution|resolution]] 1.23&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1w7c]] 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=1W7C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W7C 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]] 1.23&#8491;</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></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=1w7c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w7c OCA], [https://pdbe.org/1w7c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w7c RCSB], [https://www.ebi.ac.uk/pdbsum/1w7c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w7c ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q96X16_PICPA Q96X16_PICPA]
+== 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/w7/1w7c_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=1w7c ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structure of Pichia pastoris lysyl oxidase (PPLO) in a new crystal form has been refined at 1.23 Angstrom resolution. PPLO, a copper amine oxidase (CuAO) with a 2,4,5-trihydroxyphenylalanine quinone (TPQ) cofactor, differs from most other members of the CuAO enzyme family in having the ability to oxidize the side chain of lysine residues in a polypeptide. In the asymmetric unit of the crystals, the structure analysis has located residues 43-779 of the polypeptide chain, seven carbohydrate residues, the active-site Cu atom, an imidazole molecule bound at the active site, two buried Ca(2+) ions, five surface Mg(2+) ions, five surface Cl(-) ions and 1045 water molecules. The crystallographic residuals are R = 0.112 and R(free) = 0.146. The TPQ cofactor and several other active-site residues are poorly ordered, in contrast to the surrounding well ordered structure. A covalent cross-link is observed between two lysine residues, Lys778 and Lys66. The cross-link is likely to have been formed by the oxidation of Lys778 followed by a spontaneous reaction with Lys66. The link is modelled as dehydrolysinonorleucine.
-==About this Structure==
+The 1.23 Angstrom structure of Pichia pastoris lysyl oxidase reveals a lysine-lysine cross-link.,Duff AP, Cohen AE, Ellis PJ, Hilmer K, Langley DB, Dooley DM, Freeman HC, Guss JM Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):1073-84. Epub 2006, Aug 19. PMID:16929109<ref>PMID:16929109</ref>
-W7C is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pichia_pastoris Pichia pastoris] with NAG, CU, CA, MG, CL, TPQ and IMD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1W7C OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-The 1.23 Angstrom structure of Pichia pastoris lysyl oxidase reveals a lysine-lysine cross-link., Duff AP, Cohen AE, Ellis PJ, Hilmer K, Langley DB, Dooley DM, Freeman HC, Guss JM, Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):1073-84. Epub 2006, Aug 19. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16929109 16929109]
+</div>
-[[Category: Pichia pastoris]]
+<div class="pdbe-citations 1w7c" style="background-color:#fffaf0;"></div>
-[[Category: Protein-lysine 6-oxidase]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Cohen, A.E.]]
+__TOC__
-[[Category: Duff, A.P.]]
+</StructureSection>
-[[Category: Ellis, P.J.]]
+[[Category: Komagataella pastoris]]
-[[Category: Guss, J.M.]]
+[[Category: Large Structures]]
-[[Category: CA]]
+[[Category: Cohen AE]]
-[[Category: CL]]
+[[Category: Duff AP]]
-[[Category: CU]]
+[[Category: Ellis PJ]]
-[[Category: IMD]]
+[[Category: Guss JM]]
-[[Category: MG]]
-[[Category: NAG]]
-[[Category: TPQ]]
-[[Category: amne oxidase]]
-[[Category: copper]]
-[[Category: oxidase]]
-[[Category: oxidoreductase]]
-[[Category: quinoprotein]]
-[[Category: topaquinone enzyme]]
-[[Category: tpq]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:29:30 2007''