1c0l: Difference between revisions

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 ==D-AMINO ACID OXIDASE: STRUCTURE OF SUBSTRATE COMPLEXES AT VERY HIGH RESOLUTION REVEAL THE CHEMICAL REACTTION MECHANISM OF FLAVIN DEHYDROGENATION==
-<StructureSection load='1c0l' size='340' side='right' caption='[[1c0l]], [[Resolution|resolution]] 1.73&Aring;' scene=''>
+<StructureSection load='1c0l' size='340' side='right'caption='[[1c0l]], [[Resolution|resolution]] 1.73&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1c0l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_6016 Cbs 6016]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C0L FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1c0l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodotorula_toruloides Rhodotorula toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C0L FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FLA:TRIFLUOROALANINE'>FLA</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]] 1.73&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1c0i|1c0i]], [[1c0k|1c0k]], [[1c0p|1c0p]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FLA:TRIFLUOROALANINE'>FLA</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1c0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0l OCA], [http://pdbe.org/1c0l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1c0l RCSB], [http://www.ebi.ac.uk/pdbsum/1c0l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1c0l ProSAT]</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=1c0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0l OCA], [https://pdbe.org/1c0l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c0l RCSB], [https://www.ebi.ac.uk/pdbsum/1c0l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c0l ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/OXDA_RHOTO OXDA_RHOTO]] This enzyme can effectively convert cephalosporin C into 7-beta-(5-carboxy-5-oxopentanamido)-cephalosporinic acid.
+[https://www.uniprot.org/uniprot/OXDA_RHOTO OXDA_RHOTO] This enzyme can effectively convert cephalosporin C into 7-beta-(5-carboxy-5-oxopentanamido)-cephalosporinic acid.
 == 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/c0/1c0l_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c0/1c0l_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 20: / Line 20: @@
 </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=1c0l ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Flavin is one of the most versatile redox cofactors in nature and is used by many enzymes to perform a multitude of chemical reactions. d-Amino acid oxidase (DAAO), a member of the flavoprotein oxidase family, is regarded as a key enzyme for the understanding of the mechanism underlying flavin catalysis. The very high-resolution structures of yeast DAAO complexed with d-alanine, d-trifluoroalanine, and l-lactate (1.20, 1.47, and 1.72 A) provide strong evidence for hydride transfer as the mechanism of dehydrogenation. This is inconsistent with the alternative carbanion mechanism originally favored for this type of enzymatic reaction. The step of hydride transfer can proceed without involvement of amino acid functional groups. These structures, together with results from site-directed mutagenesis, point to orbital orientation/steering as the major factor in catalysis. A diatomic species, proposed to be a peroxide, is found at the active center and on the Re-side of the flavin. These results are of general relevance for the mechanisms of flavoproteins and lead to the proposal of a common dehydrogenation mechanism for oxidases and dehydrogenases.
-The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation.,Umhau S, Pollegioni L, Molla G, Diederichs K, Welte W, Pilone MS, Ghisla S Proc Natl Acad Sci U S A. 2000 Nov 7;97(23):12463-8. PMID:11070076<ref>PMID:11070076</ref>
+==See Also==
+*[[Amino acid oxidase 3D structures|Amino acid oxidase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1c0l" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Cbs 6016]]
+[[Category: Large Structures]]
-[[Category: Diederichs, K]]
+[[Category: Rhodotorula toruloides]]
-[[Category: Ghisla, S]]
+[[Category: Diederichs K]]
-[[Category: Molla, G]]
+[[Category: Ghisla S]]
-[[Category: Pilone, M S]]
+[[Category: Molla G]]
-[[Category: Umhau, S]]
+[[Category: Pilone MS]]
-[[Category: Welte, W]]
+[[Category: Umhau S]]
-[[Category: Flavin containing protein alpha-beta-alpha motif]]
+[[Category: Welte W]]
-[[Category: Oxidoreductase]]