PDBsum entry 1rov

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protein metals links
Oxidoreductase PDB id
Protein chain
836 a.a. *
Waters ×301
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Lipoxygenase-3 treated with cumene hydroperoxide
Structure: Seed lipoxygenase-3. Chain: a. Synonym: l-3. Ec:
Source: Glycine max. Soybean. Organism_taxid: 3847. Strain: l. Merrill cv resnick
2.00Å     R-factor:   0.221     R-free:   0.231
Authors: A.Vahedi-Faridi,P.A.Brault,P.Shah,Y.W.Kim,W.R.Dunham, M.O.Funk
Key ref: A.Vahedi-Faridi et al. (2004). Interaction between non-heme iron of lipoxygenases and cumene hydroperoxide: basis for enzyme activation, inactivation, and inhibition. J Am Chem Soc, 126, 2006-2015. PubMed id: 14971933 DOI: 10.1021/ja0390855
02-Dec-03     Release date:   16-Mar-04    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P09186  (LOX3_SOYBN) -  Seed linoleate 9S-lipoxygenase-3
857 a.a.
836 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 9 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Linoleate 9S-lipoxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Linoleate + O2 = (9S,10E,12Z)-9-hydroperoxy-10,12-octadecadienoate
+ O(2)
= (9S,10E,12Z)-9-hydroperoxy-10,12-octadecadienoate
      Cofactor: Fe cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     oxidation-reduction process   5 terms 
  Biochemical function     oxidoreductase activity     6 terms  


    Added reference    
DOI no: 10.1021/ja0390855 J Am Chem Soc 126:2006-2015 (2004)
PubMed id: 14971933  
Interaction between non-heme iron of lipoxygenases and cumene hydroperoxide: basis for enzyme activation, inactivation, and inhibition.
A.Vahedi-Faridi, P.A.Brault, P.Shah, Y.W.Kim, W.R.Dunham, M.O.Funk.
Lipoxygenase catalysis depends in a critical fashion on the redox properties of a unique mononuclear non-heme iron cofactor. The isolated enzyme contains predominantly, if not exclusively, iron(II), but the catalytically active form of the enzyme has iron(III). The activating oxidation of the iron takes place in a reaction with the hydroperoxide product of the catalyzed reaction. In a second peroxide-dependent process, lipoxygenases are also inactivated. To examine the redox activation/inactivation dichotomy in lipoxygenase chemistry, the interaction between lipoxygenase-1 (and -3) and cumene hydroperoxide was investigated. Cumene hydroperoxide was a reversible inhibitor of the reaction catalyzed by lipoxygenase-1 under standard assay conditions at high substrate concentrations. Reconciliation of the data with the currently held kinetic mechanism requires simultaneous binding of substrate and peroxide. The enzyme also was both oxidized and largely inactivated in a reaction with the peroxide in the absence of substrate. The consequences of this reaction for the enzyme included the hydroxylation at C beta of two amino acid side chains in the vicinity of the cofactor, Trp and Leu. The modifications were identified by mass spectrometry and X-ray crystallography. The peroxide-induced oxidation of iron was also accompanied by a subtle rearrangement in the coordination sphere of the non-heme iron atom. Since the enzyme retains catalytic activity, albeit diminished, after treatment with cumene hydroperoxide, the structure of the iron site may reflect the catalytically relevant form of the cofactor.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19683507 J.Rapp, S.Xu, A.M.Sharp, W.P.Griffith, Y.W.Kim, and M.O.Funk (2009).
EPR spectroscopy and electrospray ionization mass spectrometry reveal distinctive features of the iron site in leukocyte 12-lipoxygenase.
  Arch Biochem Biophys, 490, 50-56.  
17879349 A.M.Peariso, K.M.Nicholson, R.Benjamin Jones, K.B.Green-Church, and M.O.Funk (2008).
Electrospray ionization mass spectrometry of soybean lipoxygenases: N-terminal acetylation, chemical modification, and solution conformation.
  Proteins, 70, 650-658.  
18478283 J.E.Mendieta-Wejebe, M.C.Rosales-Hernández, H.Rios, J.Trujillo-Ferrara, G.López-Pérez, F.Tamay-Cach, R.Ramos-Morales, and J.Correa-Basurto (2008).
Comparing the electronic properties and docking calculations of heme derivatives on CYP2B4.
  J Mol Model, 14, 537-545.  
16790932 E.Skrzypczak-Jankun, O.Y.Borbulevych, M.I.Zavodszky, M.R.Baranski, K.Padmanabhan, V.Petricek, and J.Jankun (2006).
Effect of crystal freezing and small-molecule binding on internal cavity size in a large protein: X-ray and docking studies of lipoxygenase at ambient and low temperature at 2.0 A resolution.
  Acta Crystallogr D Biol Crystallogr, 62, 766-775.
PDB codes: 1rrh 1rrl
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