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1ve9

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Porcine kidney D-amino acid oxidase

Structural highlights

1ve9 is a 2 chain structure with sequence from Sus scrofa. This structure supersedes the now removed PDB entry 1aa8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
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.

Publication Abstract from PubMed

The X-ray crystallographic structure of porcine kidney D-amino acid oxidase, which had been expressed in Escherichia coli transformed with a vector containing DAO cDNA, was determined by the isomorphous replacement method for the complex form with benzoate. The known amino acid sequence, FAD and benzoate were fitted to an electron density map of 3.0 A resolution with an R-factor of 21.0%. The overall dimeric structure exhibits an elongated ellipsoidal framework. The prosthetic group, FAD, was found to be in an extended conformation, the isoalloxazine ring being buried in the protein core. The ADP moiety of FAD was located in the typical beta alpha beta dinucleotide binding motif, with the alpha-helix dipole stabilizing the pyrophosphate negative charge. The substrate analog, benzoate, is located on the re-face of the isoalloxazine ring, while the si-face is blocked by hydrophobic residues. The carboxylate group of benzoate is ion-paired with the Arg283 side chain and is within interacting distance with the hydroxy moiety of Tyr228. The phenol ring of Tyr224 is located just above the benzene ring of benzoate, implying the importance of this residue for catalysis. There is no positive charge or alpha-helix dipole near N(1) of flavin. Hydrogen bonds were observed at C(2) = O, N(3)-H, C(4) = O, and N(5) of the flavin ring.

Three-dimensional structure of porcine kidney D-amino acid oxidase at 3.0 A resolution.,Mizutani H, Miyahara I, Hirotsu K, Nishina Y, Shiga K, Setoyama C, Miura R J Biochem. 1996 Jul;120(1):14-7. PMID:8864836^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Mizutani H, Miyahara I, Hirotsu K, Nishina Y, Shiga K, Setoyama C, Miura R. Three-dimensional structure of porcine kidney D-amino acid oxidase at 3.0 A resolution. J Biochem. 1996 Jul;120(1):14-7. PMID:8864836

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ve9"

@@ Line 3: / Line 3: @@
 <StructureSection load='1ve9' size='340' side='right'caption='[[1ve9]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ve9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pig Pig]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1aa8 1aa8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VE9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VE9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ve9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1aa8 1aa8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VE9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VE9 FirstGlance]. <br>
-</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>
+</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>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/D-amino-acid_oxidase D-amino-acid oxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.3 1.4.3.3] </span></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=1ve9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ve9 OCA], [https://pdbe.org/1ve9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ve9 RCSB], [https://www.ebi.ac.uk/pdbsum/1ve9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ve9 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.
+[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]]
@@ Line 36: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: D-amino-acid oxidase]]
 [[Category: Large Structures]]
-[[Category: Pig]]
+[[Category: Sus scrofa]]
-[[Category: Hirotsu, K]]
+[[Category: Hirotsu K]]
-[[Category: Miura, R]]
+[[Category: Miura R]]
-[[Category: Miyahara, I]]
+[[Category: Miyahara I]]
-[[Category: Mizutani, H]]
+[[Category: Mizutani H]]
-[[Category: Nishina, Y]]
+[[Category: Nishina Y]]
-[[Category: Setoyama, C]]
+[[Category: Setoyama C]]
-[[Category: Shiga, K]]
+[[Category: Shiga K]]
-[[Category: D-amino acid]]
-[[Category: Fad]]
-[[Category: Oxidase]]
-[[Category: Oxidoreductase]]

1ve9

From Proteopedia

Current revision

Porcine kidney D-amino acid oxidase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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