spacer
spacer

PDBsum entry 1aa8

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidase PDB id
1aa8
Jmol
Contents
Protein chains
340 a.a.
Ligands
FAD ×2
BEZ ×2
Waters ×468
Superseded by: 1ve9
PDB id:
1aa8
Name: Oxidase
Title: Porcine kidney d-amino acid oxidase
Structure: D-amino acid oxidase. Chain: a, b. Engineered: yes
Source: Sus scrofa. Pig. Organ: kidney. Expressed in: escherichia coli
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.207     R-free:   0.288
Authors: H.Mizutani,I.Miyahara,K.Hirotsu,Y.Nishina,K.Shiga, C.Setoyama,R.Miura
Key ref: H.Mizutani et al. (1996). Three-dimensional structure of porcine kidney D-amino acid oxidase at 3.0 A resolution. J Biochem, 120, 14-17. PubMed id: 8864836
Date:
25-Jan-97     Release date:   21-Apr-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00371  (OXDA_PIG) -  D-amino-acid oxidase
Seq:
Struc:
347 a.a.
340 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.4.3.3  - D-amino-acid oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Cephalosporin Biosynthesis
      Reaction: A D-amino acid + H2O + O2 = a 2-oxo acid + NH3 + H2O2
D-amino acid
+ H(2)O
+ O(2)
= 2-oxo acid
+ NH(3)
+ H(2)O(2)
      Cofactor: FAD
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
J Biochem 120:14-17 (1996)
PubMed id: 8864836  
 
 
Three-dimensional structure of porcine kidney D-amino acid oxidase at 3.0 A resolution.
H.Mizutani, I.Miyahara, K.Hirotsu, Y.Nishina, K.Shiga, C.Setoyama, R.Miura.
 
  ABSTRACT  
 
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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20567862 M.Katane, Y.Saitoh, K.Maeda, T.Hanai, M.Sekine, T.Furuchi, and H.Homma (2011).
Role of the active site residues arginine-216 and arginine-237 in the substrate specificity of mammalian D-aspartate oxidase.
  Amino Acids, 40, 467-476.  
  20514350 H.Soetedjo, M.F.Mora, and C.D.Garcia (2010).
Optical Properties of Single-Wall Carbon Nanotube Films Deposited on Si/SiO(2) Wafers.
  Thin Solid Films, 518, 3954-3959.  
20195697 L.Pollegioni, and S.Sacchi (2010).
Metabolism of the neuromodulator D-serine.
  Cell Mol Life Sci, 67, 2387-2404.  
20564562 M.Katane, and H.Homma (2010).
D-aspartate oxidase: the sole catabolic enzyme acting on free D-aspartate in mammals.
  Chem Biodivers, 7, 1435-1449.  
19651103 P.F.Fitzpatrick (2010).
Oxidation of amines by flavoproteins.
  Arch Biochem Biophys, 493, 13-25.  
19267668 A.Gholizadeh, and B.B.Kohnehrouz (2009).
Molecular cloning and expression in Escherichia coli of an active fused Zea mays L. D-amino acid oxidase.
  Biochemistry (Mosc), 74, 137-144.  
19132842 M.F.Mora, C.E.Giacomelli, and C.D.Garcia (2009).
Interaction of D-amino acid oxidase with carbon nanotubes: implications in the design of biosensors.
  Anal Chem, 81, 1016-1022.  
16245349 M.Bakke, C.Setoyama, R.Miura, and N.Kajiyama (2006).
Thermostabilization of porcine kidney D-amino acid oxidase by a single amino acid substitution.
  Biotechnol Bioeng, 93, 1023-1027.  
17088322 T.Kawazoe, H.Tsuge, M.S.Pilone, and K.Fukui (2006).
Crystal structure of human D-amino acid oxidase: context-dependent variability of the backbone conformation of the VAAGL hydrophobic stretch located at the si-face of the flavin ring.
  Protein Sci, 15, 2708-2717.
PDB code: 2du8
15057273 M.Koch, C.Breithaupt, R.Kiefersauer, J.Freigang, R.Huber, and A.Messerschmidt (2004).
Crystal structure of protoporphyrinogen IX oxidase: a key enzyme in haem and chlorophyll biosynthesis.
  EMBO J, 23, 1720-1728.
PDB code: 1sez
14674755 G.Wille, M.Ritter, R.Friedemann, W.Mäntele, and G.Hübner (2003).
Redox-triggered FTIR difference spectra of FAD in aqueous solution and bound to flavoproteins.
  Biochemistry, 42, 14814-14821.  
11514662 O.Dym, and D.Eisenberg (2001).
Sequence-structure analysis of FAD-containing proteins.
  Protein Sci, 10, 1712-1728.  
11895118 R.Miura (2001).
Versatility and specificity in flavoenzymes: control mechanisms of flavin reactivity.
  Chem Rec, 1, 183-194.  
11157233 Y.Liu, T.M.Louie, J.Payne, J.Bohuslavek, H.Bolton, and L.Xun (2001).
Identification, purification, and characterization of iminodiacetate oxidase from the EDTA-degrading bacterium BNC1.
  Appl Environ Microbiol, 67, 696-701.  
10716694 A.A.Raibekas, K.Fukui, and V.Massey (2000).
Design and properties of human D-amino acid oxidase with covalently attached flavin.
  Proc Natl Acad Sci U S A, 97, 3089-3093.  
10962107 E.Varela, M.Jesús Martínez, and A.T.Martínez (2000).
Aryl-alcohol oxidase protein sequence: a comparison with glucose oxidase and other FAD oxidoreductases.
  Biochim Biophys Acta, 1481, 202-208.
PDB code: 1qjn
10706608 K.Yorita, H.Misaki, B.A.Palfey, and V.Massey (2000).
On the interpretation of quantitative structure-function activity relationship data for lactate oxidase.
  Proc Natl Acad Sci U S A, 97, 2480-2485.  
10944103 P.D.Pawelek, J.Cheah, R.Coulombe, P.Macheroux, S.Ghisla, and A.Vrielink (2000).
The structure of L-amino acid oxidase reveals the substrate trajectory into an enantiomerically conserved active site.
  EMBO J, 19, 4204-4215.
PDB codes: 1f8r 1f8s
11070076 S.Umhau, L.Pollegioni, G.Molla, K.Diederichs, W.Welte, M.S.Pilone, and S.Ghisla (2000).
The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation.
  Proc Natl Acad Sci U S A, 97, 12463-12468.
PDB codes: 1c0k 1c0l 1c0p
10425677 A.Mattevi, G.Tedeschi, L.Bacchella, A.Coda, A.Negri, and S.Ronchi (1999).
Structure of L-aspartate oxidase: implications for the succinate dehydrogenase/fumarate reductase oxidoreductase family.
  Structure, 7, 745-756.
PDB code: 1chu
  10427080 M.Gabler, and L.Fischer (1999).
Production of a new D-amino acid oxidase from the fungus Fusarium oxysporum.
  Appl Environ Microbiol, 65, 3750-3753.  
10368302 P.Trickey, M.A.Wagner, M.S.Jorns, and F.S.Mathews (1999).
Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme.
  Structure, 7, 331-345.
PDB codes: 1b3m 1l9f 2gb0
9546198 A.Mattevi (1998).
The PHBH fold: not only flavoenzymes.
  Biophys Chem, 70, 217-222.  
  9684885 K.S.Rao, and F.Lederer (1998).
About the pKa of the active-site histidine in flavocytochrome b2 (yeast L-lactate dehydrogenase).
  Protein Sci, 7, 1531-1537.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.