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1c0p

From Proteopedia

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[[Image:1c0p.jpg|left|200px]]
 
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{{Structure
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==D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OCCUPIED BIATOMIC SPECIES==
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|PDB= 1c0p |SIZE=350|CAPTION= <scene name='initialview01'>1c0p</scene>, resolution 1.2&Aring;
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<StructureSection load='1c0p' size='340' side='right'caption='[[1c0p]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene>
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<table><tr><td colspan='2'>[[1c0p]] 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=1C0P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C0P FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/D-amino-acid_oxidase D-amino-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.3 1.4.3.3] </span>
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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]] 1.2&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></td></tr>
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|DOMAIN=
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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=1c0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0p OCA], [https://pdbe.org/1c0p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c0p RCSB], [https://www.ebi.ac.uk/pdbsum/1c0p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c0p ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1c0l|1C0L]], [[1c0k|1C0K]], [[1c0i|1C0I]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1c0p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0p OCA], [http://www.ebi.ac.uk/pdbsum/1c0p PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1c0p RCSB]</span>
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== Function ==
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}}
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[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.
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== Evolutionary Conservation ==
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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/c0/1c0p_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=1c0p ConSurf].
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<div style="clear:both"></div>
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'''D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OCCUPIED BIATOMIC SPECIES'''
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==See Also==
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*[[Amino acid oxidase 3D structures|Amino acid oxidase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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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.
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[[Category: Large Structures]]
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[[Category: Rhodotorula toruloides]]
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==About this Structure==
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[[Category: Diederichs K]]
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1C0P is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rhodosporidium_toruloides Rhodosporidium toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0P OCA].
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[[Category: Ghisla S]]
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[[Category: Molla G]]
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==Reference==
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[[Category: Pilone SM]]
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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:[http://www.ncbi.nlm.nih.gov/pubmed/11070076 11070076]
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[[Category: Pollegioni L]]
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[[Category: D-amino-acid oxidase]]
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[[Category: Umhau S]]
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[[Category: Rhodosporidium toruloides]]
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[[Category: Welte W]]
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[[Category: Single protein]]
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[[Category: Diederichs, K.]]
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[[Category: Ghisla, S.]]
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[[Category: Molla, G.]]
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[[Category: Pilone, S M.]]
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[[Category: Pollegioni, L.]]
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[[Category: Umhau, S.]]
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[[Category: Welte, W.]]
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[[Category: alpha-beta-alpha motif]]
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[[Category: flavin containing protein]]
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[[Category: oxidase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:12:16 2008''
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Current revision

D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OCCUPIED BIATOMIC SPECIES

PDB ID 1c0p

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