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PDBsum entry 1an9

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
1an9
Jmol
Contents
Protein chains
340 a.a. *
Ligands
FAD ×2
BE2 ×2
Waters ×112
* Residue conservation analysis
PDB id:
1an9
Name: Oxidoreductase
Title: D-amino acid oxidase complex with o-aminobenzoate
Structure: D-amino acid oxidase. Chain: a, b. Engineered: yes
Source: Sus scrofa. Pig. Organism_taxid: 9823. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.50Å     R-factor:   0.201     R-free:   0.260
Authors: R.Miura,C.Setoyama,Y.Nishina,K.Shiga,H.Mizutani,I.Miyahara, K.Hirotsu
Key ref: R.Miura et al. (1997). Structural and mechanistic studies on D-amino acid oxidase x substrate complex: implications of the crystal structure of enzyme x substrate analog complex. J Biochem, 122, 825-833. PubMed id: 9399588
Date:
28-Jun-97     Release date:   12-Nov-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
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   4 terms 
  Biological process     D-serine catabolic process   7 terms 
  Biochemical function     FAD binding     7 terms  

 

 
    reference    
 
 
J Biochem 122:825-833 (1997)
PubMed id: 9399588  
 
 
Structural and mechanistic studies on D-amino acid oxidase x substrate complex: implications of the crystal structure of enzyme x substrate analog complex.
R.Miura, C.Setoyama, Y.Nishina, K.Shiga, H.Mizutani, I.Miyahara, K.Hirotsu.
 
  ABSTRACT  
 
As an extension of our recent X-ray crystallographic determination of the tertiary structure of D-amino acid oxidase (DAO) [Mizutani, H. et al. (1996) J. Biochem. 120, 14-17], we solved the crystal structure of the complex of DAO with a substrate analog, o-aminobenzoate (OAB). The alignment between flavin and OAB in the crystal structure of the complex is consistent with charge-transfer interaction through the overlap between the highest occupied molecular orbital of OAB and the lowest unoccupied molecular orbital of flavin. Starting with the atomic coordinates of this complex as the initial model, we carried out molecular mechanics simulation for the DAO-D-leucine complex and thus obtained a model for the enzyme-substrate complex. According to the enzyme-substrate complex model, the alpha-proton is pointed toward N(5) of flavin while the lone-pair of the substrate amino group can approach C(4a) of flavin within an interacting distance. This model as well as DAO-OAB complex enables the evaluation of the substrate-flavin interaction prior to electron transfer from the substrate to flavin and provides two possible mechanisms for the reductive-half reaction of DAO, i.e., the electron-proton-electron transfer mechanism and the ionic mechanism.
 

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.  
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.  
17697998 C.J.Carrell, R.C.Bruckner, D.Venci, G.Zhao, M.S.Jorns, and F.S.Mathews (2007).
NikD, an unusual amino acid oxidase essential for nikkomycin biosynthesis: structures of closed and open forms at 1.15 and 1.90 A resolution.
  Structure, 15, 928-941.
PDB codes: 2oln 2olo 2q6u
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
11258887 C.Binda, R.Angelini, R.Federico, P.Ascenzi, and A.Mattevi (2001).
Structural bases for inhibitor binding and catalysis in polyamine oxidase.
  Biochemistry, 40, 2766-2776.
PDB codes: 1h81 1h82 1h83 1h84 1h86
10992285 H.Yurimoto, T.Hasegawa, Y.Sakai, and N.Kato (2000).
Physiological role of the D-amino acid oxidase gene, DAO1, in carbon and nitrogen metabolism in the methylotrophic yeast Candida boidinii.
  Yeast, 16, 1217-1227.  
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
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
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 codes are shown on the right.