spacer
spacer

PDBsum entry 2iid

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
2iid
Jmol
Contents
Protein chains
483 a.a. *
Ligands
NAG-FUC ×3
NAG ×5
PHE ×4
FAD ×4
Waters ×2085
* Residue conservation analysis
PDB id:
2iid
Name: Oxidoreductase
Title: Structure of l-amino acid oxidase from calloselasma rhodosto complex with l-phenylalanine
Structure: L-amino-acid oxidase. Chain: a, b, c, d. Synonym: lao, laao, apoxin i. Ec: 1.4.3.2
Source: Calloselasma rhodostoma. Malayan pit viper. Organism_taxid: 8717. Secretion: venom
Biol. unit: Tetramer (from PQS)
Resolution:
1.80Å     R-factor:   0.174     R-free:   0.210
Authors: I.M.Moustafa,S.Foster,A.Y.Lyubimov,A.Vrielink
Key ref:
I.M.Moustafa et al. (2006). Crystal structure of LAAO from Calloselasma rhodostoma with an L-phenylalanine substrate: insights into structure and mechanism. J Mol Biol, 364, 991. PubMed id: 17046020 DOI: 10.1016/j.jmb.2006.09.032
Date:
27-Sep-06     Release date:   31-Oct-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P81382  (OXLA_CALRH) -  L-amino-acid oxidase
Seq:
Struc:
516 a.a.
483 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.4.3.2  - L-amino-acid oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: An L-amino acid + H2O + O2 = a 2-oxo acid + NH3 + H2O2
L-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     extracellular region   1 term 
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     oxidoreductase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.jmb.2006.09.032 J Mol Biol 364:991 (2006)
PubMed id: 17046020  
 
 
Crystal structure of LAAO from Calloselasma rhodostoma with an L-phenylalanine substrate: insights into structure and mechanism.
I.M.Moustafa, S.Foster, A.Y.Lyubimov, A.Vrielink.
 
  ABSTRACT  
 
L-Amino acid oxidase is a dimeric glycosylated flavoenzyme, a major constituent of the venom-from the snake Calloselasma rhodostoma. The enzyme exhibits apoptosis inducing effects as well as antibacterial and anti-HIV activities. The structure of l-amino acid oxidase with its substrate (L-phenylalanine) has been refined to a resolution of 1.8 A. The complex structure reveals the substrate bound to the reduced flavin (FADred). Alternative conformations for the key residues His223 and Arg322 are evident, suggesting a dynamic active site. Furthermore, conformational changes are apparent for the isoalloxazine ring; the three-ring system exhibits more bending around the N5-N10 axis compared to the oxidized flavin. The implications of the observed dynamics on the mechanism of catalysis are discussed. Inspection of buried surfaces in the enzyme reveals a Y-shaped channel system extending from the external surface of the protein to the active site. One portion of this channel may serve as the entry path for O2 during the oxidative half-reaction. The second region, separated from the proposed O2 channel by the N terminus (residues 8-16) of the protein, may play a role in H2O2 release. Interestingly, the latter portion of the channel would direct the H2O2 product to the exterior surface of the protein, near the glycan moiety, thought to anchor the enzyme to the host cell. This channel location may explain the ability of the enzyme to localize H2O2 to the targeted cell and thus induce the apoptotic effect.
 
  Selected figure(s)  
 
Figure 2.
Figure 5.
Figure 5. Reaction mechanism for the oxidation of l-phenylalanine by l-amino acid oxidase. The substrate is shown in thick bonds. Two conformations for His223 are included as labeled.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 364, 991-0) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20938508 D.Georgieva, M.Murakami, M.Perband, R.Arni, and C.Betzel (2011).
The structure of a native l-amino acid oxidase, the major component of the Vipera ammodytes ammodytes venomic, reveals dynamic active site and quaternary structure stabilization by divalent ions.
  Mol Biosyst, 7, 379-384.  
21298676 J.O.Baek, J.W.Seo, O.Kwon, S.I.Seong, I.H.Kim, and C.H.Kim (2011).
Expression and characterization of a second L-amino acid deaminase isolated from Proteus mirabilis in Escherichia coli.
  J Basic Microbiol, 51, 129-135.  
20878154 A.L.Hughes (2010).
Origin and diversification of the L-amino oxidase family in innate immune defenses of animals.
  Immunogenetics, 62, 753-759.  
19531050 J.Arima, C.Sasaki, C.Sakaguchi, H.Mizuno, T.Tamura, A.Kashima, H.Kusakabe, S.Sugio, and K.Inagaki (2009).
Structural characterization of L-glutamate oxidase from Streptomyces sp. X-119-6.
  FEBS J, 276, 3894-3903.
PDB code: 2e1m
19815515 Y.Tu, P.Xiu, R.Wan, J.Hu, R.Zhou, and H.Fang (2009).
Water-mediated signal multiplication with Y-shaped carbon nanotubes.
  Proc Natl Acad Sci U S A, 106, 18120-18124.  
18186483 A.Ilari, A.Bonamore, S.Franceschini, A.Fiorillo, A.Boffi, and G.Colotti (2008).
The X-ray structure of N-methyltryptophan oxidase reveals the structural determinants of substrate specificity.
  Proteins, 71, 2065-2075.
PDB code: 2uzz
  18931435 D.Georgieva, A.Kardas, F.Buck, M.Perbandt, and C.Betzel (2008).
Isolation, crystallization and preliminary X-ray diffraction analysis of L-amino-acid oxidase from Vipera ammodytes ammodytes venom.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 918-921.  
19086859 D.Georgieva, R.K.Arni, and C.Betzel (2008).
Proteome analysis of snake venom toxins: pharmacological insights.
  Expert Rev Proteomics, 5, 787-797.  
18417467 K.Ida, M.Kurabayashi, M.Suguro, Y.Hiruma, T.Hikima, M.Yamomoto, and H.Suzuki (2008).
Structural basis of proteolytic activation of L-phenylalanine oxidase from Pseudomonas sp. P-501.
  J Biol Chem, 283, 16584-16590.
PDB codes: 2yr4 2yr5 2yr6
18410129 L.Chen, A.Y.Lyubimov, L.Brammer, A.Vrielink, and N.S.Sampson (2008).
The binding and release of oxygen and hydrogen peroxide are directed by a hydrophobic tunnel in cholesterol oxidase.
  Biochemistry, 47, 5368-5377.
PDB code: 3cnj
18384385 S.Mandal, and D.Bhattacharyya (2008).
Two L-amino acid oxidase isoenzymes from Russell's viper (Daboia russelli russelli) venom with different mechanisms of inhibition by substrate analogs.
  FEBS J, 275, 2078-2095.  
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.