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1evi

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[[Image:1evi.gif|left|200px]]
 
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{{Structure
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==THREE-DIMENSIONAL STRUCTURE OF THE PURPLE INTERMEDIATE OF PORCINE KIDNEY D-AMINO ACID OXIDASE==
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|PDB= 1evi |SIZE=350|CAPTION= <scene name='initialview01'>1evi</scene>, resolution 2.5&Aring;
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<StructureSection load='1evi' size='340' side='right'caption='[[1evi]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=2PC:3,4-DIHYDRO-2H-PYRROLIUM-5-CARBOXYLATE'>2PC</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>
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<table><tr><td colspan='2'>[[1evi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EVI 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]] 2.5&#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=2PC:3,4-DIHYDRO-2H-PYRROLIUM-5-CARBOXYLATE'>2PC</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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=1evi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evi OCA], [https://pdbe.org/1evi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1evi RCSB], [https://www.ebi.ac.uk/pdbsum/1evi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1evi ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1aa8|1AA8]], [[1an9|1AN9]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1evi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1evi OCA], [http://www.ebi.ac.uk/pdbsum/1evi PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1evi RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/OXDA_PIG OXDA_PIG] Regulates the level of the neuromodulator D-serine in the brain. Has high activity towards D-DOPA and contributes to dopamine synthesis. Could act as a detoxifying agent which removes D-amino acids accumulated during aging. Acts on a variety of D-amino acids with a preference for those having small hydrophobic side chains followed by those bearing polar, aromatic, and basic groups. Does not act on acidic amino acids.
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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/ev/1evi_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=1evi ConSurf].
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<div style="clear:both"></div>
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'''THREE-DIMENSIONAL STRUCTURE OF THE PURPLE INTERMEDIATE OF PORCINE KIDNEY D-AMINO ACID OXIDASE'''
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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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The three-dimensional structure of the purple intermediate of porcine kidney D-amino acid oxidase (DAO) was solved by cryo-X-ray crystallography; the purple intermediate is known to comprise a complex between the dehydrogenated product, an imino acid, and the reduced form of DAO. The crystalline purple intermediate was obtained by anaerobically soaking crystals of oxidized DAO in a buffer containing excess D-proline as the substrate. The dehydrogenated product, delta(1)-pyrrolidine-2-carboxylate (DPC), is found sandwiched between the phenol ring of Tyr 224 and the planar reduced flavin ring. The cationic protonated imino nitrogen is within hydrogen-bonding distance of the backbone carbonyl oxygen of Gly 313. The carboxyl group of DPC is recognized by the Arg 283 guanidino and Tyr 228 hydroxyl groups through ion-pairing and hydrogen-bonding, respectively. The (+)HN=C double bond of DPC overlaps the N(5)-C(4a) bond of reduced flavin. The electrostatic effect of the cationic nitrogen of DPC is suggested to shift the resonance hybridization of anionic reduced flavin toward a canonical form with a negative charge at C(4a), thereby augmenting the electron density at C(4a), from which electrons are transferred to molecular oxygen during reoxidation of reduced flavin. The reactivity of reduced flavin in the purple intermediate, therefore, is enhanced through the alignment of DPC with respect to reduced flavin.
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[[Category: Large Structures]]
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==About this Structure==
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1EVI is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EVI OCA].
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==Reference==
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Three-dimensional structure of the purple intermediate of porcine kidney D-amino acid oxidase. Optimization of the oxidative half-reaction through alignment of the product with reduced flavin., Mizutani H, Miyahara I, Hirotsu K, Nishina Y, Shiga K, Setoyama C, Miura R, J Biochem. 2000 Jul;128(1):73-81. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10876160 10876160]
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[[Category: D-amino-acid oxidase]]
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[[Category: Single protein]]
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[[Category: Sus scrofa]]
[[Category: Sus scrofa]]
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[[Category: Hirotsu, K.]]
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[[Category: Hirotsu K]]
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[[Category: Miura, R.]]
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[[Category: Miura R]]
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[[Category: Miyahara, I.]]
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[[Category: Miyahara I]]
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[[Category: Mizutani, H.]]
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[[Category: Mizutani H]]
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[[Category: Nishina, Y.]]
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[[Category: Nishina Y]]
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[[Category: Setoyama, C.]]
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[[Category: Setoyama C]]
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[[Category: Shiga, K.]]
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[[Category: Shiga K]]
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[[Category: flavoenzyme]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:10:29 2008''
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Current revision

THREE-DIMENSIONAL STRUCTURE OF THE PURPLE INTERMEDIATE OF PORCINE KIDNEY D-AMINO ACID OXIDASE

PDB ID 1evi

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