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New page: left|200px<br /><applet load="1kif" size="450" color="white" frame="true" align="right" spinBox="true" caption="1kif, resolution 2.6Å" /> '''D-AMINO ACID OXIDASE ...
 
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[[Image:1kif.gif|left|200px]]<br /><applet load="1kif" size="450" color="white" frame="true" align="right" spinBox="true"
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'''D-AMINO ACID OXIDASE FROM PIG KIDNEY'''<br />


==Overview==
==D-AMINO ACID OXIDASE FROM PIG KIDNEY==
D-amino acid oxidase is the prototype of the FAD-dependent oxidases. It, catalyses the oxidation of D-amino acids to the corresponding, alpha-ketoacids. The reducing equivalents are transferred to molecular, oxygen with production of hydrogen peroxide. We have solved the crystal, structure of the complex of D-amino acid oxidase with benzoate, a, competitive inhibitor of the substrate, by single isomorphous replacement, and eightfold averaging. Each monomer is formed by two domains with an, overall topology similar to that of p-hydroxybenzoate hydroxylase. The, benzoate molecule lays parallel to the flavin ring and is held in position, by a salt bridge with Arg-283. Analysis of the active site shows that no, side chains are properly positioned to act as the postulated base required, for the catalytic carboanion mechanism. On the contrary, the benzoate, binding mode suggests a direct transfer of the substrate alpha-hydrogen to, the flavin during the enzyme reductive half-reaction.The active site Of, D-amino acid oxidase exhibits a striking similarity with that of, flavocytochrome b2, a structurally unrelated FMN-dependent flavoenzyme., The active site groups (if these two enzymes are in fact superimposable, once the mirror-image of the flavocytochrome b2 active site is generated, with respect to the flavin plane. Therefore, the catalytic sites of, D-amino acid oxidase and flavocytochrome b2 appear to have converged to a, highly similar but enantiomeric architecture in order to catalvze similar, reactions (oxidation of alpha-amino acids or alpha-hydroxy acids), although with opposite stereochemistry.
<StructureSection load='1kif' size='340' side='right'caption='[[1kif]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1kif]] is a 8 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=1KIF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KIF 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]] 2.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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=1kif FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kif OCA], [https://pdbe.org/1kif PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kif RCSB], [https://www.ebi.ac.uk/pdbsum/1kif PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kif ProSAT]</span></td></tr>
</table>
== Function ==
[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.
== 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/ki/1kif_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=1kif ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1KIF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa] with FAD and BEZ as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KIF OCA].
*[[Amino acid oxidase 3D structures|Amino acid oxidase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Crystal structure of D-amino acid oxidase: a case of active site mirror-image convergent evolution with flavocytochrome b2., Mattevi A, Vanoni MA, Todone F, Rizzi M, Teplyakov A, Coda A, Bolognesi M, Curti B, Proc Natl Acad Sci U S A. 1996 Jul 23;93(15):7496-501. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8755502 8755502]
[[Category: Large Structures]]
[[Category: D-amino-acid oxidase]]
[[Category: Single protein]]
[[Category: Sus scrofa]]
[[Category: Sus scrofa]]
[[Category: Mattevi, A.]]
[[Category: Mattevi A]]
[[Category: Todone, F.]]
[[Category: Todone F]]
[[Category: BEZ]]
[[Category: FAD]]
[[Category: fad cofactor]]
[[Category: flavoenzyme]]
[[Category: oxidase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:16:06 2007''

Latest revision as of 10:25, 14 February 2024

D-AMINO ACID OXIDASE FROM PIG KIDNEYD-AMINO ACID OXIDASE FROM PIG KIDNEY

Structural highlights

1kif is a 8 chain structure with sequence from Sus scrofa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.6Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1kif, resolution 2.60Å

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