1f8r: Difference between revisions

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 ==CRYSTAL STRUCTURE OF L-AMINO ACID OXIDASE FROM CALLOSELASMA RHODOSTOMA COMPLEXED WITH CITRATE==
-<StructureSection load='1f8r' size='340' side='right' caption='[[1f8r]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='1f8r' size='340' side='right'caption='[[1f8r]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1f8r]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Calloselasma_rhodostoma Calloselasma rhodostoma]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F8R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F8R FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1f8r]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Calloselasma_rhodostoma Calloselasma rhodostoma]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F8R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1F8R FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene><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]] 2&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1f8s|1f8s]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-amino-acid_oxidase L-amino-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.2 1.4.3.2] </span></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=1f8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f8r OCA], [https://pdbe.org/1f8r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1f8r RCSB], [https://www.ebi.ac.uk/pdbsum/1f8r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1f8r ProSAT]</span></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f8r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1f8r RCSB], [http://www.ebi.ac.uk/pdbsum/1f8r PDBsum]</span></td></tr>
+</table>
-<table>
+== Function ==
+[https://www.uniprot.org/uniprot/OXLA_CALRH OXLA_CALRH] Catalyzes an oxidative deamination of predominantly hydrophobic and aromatic L-amino acids, thus producing hydrogen peroxide that may contribute to the diverse toxic effects of this enzyme. Exhibits diverse biological activities, such as hemorrhage, hemolysis, edema, apoptosis of vascular endothelial cells or tumor cell lines, antibacterial and antiparasitic activities, as well as regulation of platelet aggregation. Its effect on platelets is controversial, since it either induces aggregation or inhibits agonist-induced aggregation. These different effects are probably due to different experimental conditions (By similarity).
 == 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/f8/1f8r_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f8/1f8r_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1f8r ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The structure of L-amino acid oxidase (LAAO) from Calloselasma rhodostoma has been determined to 2.0 A resolution in the presence of two ligands: citrate and o-aminobenzoate (AB). The protomer consists of three domains: an FAD-binding domain, a substrate-binding domain and a helical domain. The interface between the substrate-binding and helical domains forms a 25 A long funnel, which provides access to the active site. Three AB molecules are visible within the funnel of the LAAO-AB complex; their orientations suggest the trajectory of the substrate to the active site. The innermost AB molecule makes hydrogen bond contacts with the active site residues, Arg90 and Gly464, and the aromatic portion of the ligand is situated in a hydrophobic pocket. These contacts are proposed to mimic those of the natural substrate. Comparison of LAAO with the structure of mammalian D-amino acid oxidase reveals significant differences in their modes of substrate entry. Furthermore, a mirror-symmetrical relationship between the two substrate-binding sites is observed which facilitates enantiomeric selectivity while preserving a common arrangement of the atoms involved in catalysis.
-The structure of L-amino acid oxidase reveals the substrate trajectory into an enantiomerically conserved active site.,Pawelek PD, Cheah J, Coulombe R, Macheroux P, Ghisla S, Vrielink A EMBO J. 2000 Aug 15;19(16):4204-15. PMID:10944103<ref>PMID:10944103</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Amino acid oxidase|Amino acid oxidase]]
+*[[Amino acid oxidase 3D structures|Amino acid oxidase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Calloselasma rhodostoma]]
-[[Category: L-amino-acid oxidase]]
+[[Category: Large Structures]]
-[[Category: Cheah, J.]]
+[[Category: Cheah J]]
-[[Category: Coulombe, R.]]
+[[Category: Coulombe R]]
-[[Category: Ghisla, S.]]
+[[Category: Ghisla S]]
-[[Category: Macheroux, P.]]
+[[Category: Macheroux P]]
-[[Category: Pawelek, P D.]]
+[[Category: Pawelek PD]]
-[[Category: Vrielink, A.]]
+[[Category: Vrielink A]]
-[[Category: Active site funnel]]
-[[Category: Enantiomeric specificity]]
-[[Category: Fad-binding domain]]
-[[Category: Flavoenzyme]]
-[[Category: Helical domain]]
-[[Category: Oxidase]]
-[[Category: Oxidoreductase]]