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PDBsum entry 3fg1

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protein ligands metals Protein-protein interface(s) links
Oxidoreductase PDB id
3fg1
Jmol
Contents
Protein chains
684 a.a. *
Ligands
ACY ×23
GOL ×23
Metals
_CA ×8
_CL ×6
FE2 ×4
Waters ×2667
* Residue conservation analysis
PDB id:
3fg1
Name: Oxidoreductase
Title: Crystal structure of delta413-417:gs lox
Structure: Allene oxide synthase-lipoxygenase protein. Chain: a, b, c, d. Fragment: arachidonate 8r-lipoxygenase: unp residues 374-10 synonym: allene oxide synthase, hydroperoxidehydrase, arach lipoxygenase. Engineered: yes. Mutation: yes
Source: Plexaura homomalla. Black sea rod. Organism_taxid: 47982. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.85Å     R-factor:   0.176     R-free:   0.209
Authors: D.B.Neau,M.E.Newcomer
Key ref: D.B.Neau et al. (2009). The 1.85 A structure of an 8R-lipoxygenase suggests a general model for lipoxygenase product specificity. Biochemistry, 48, 7906-7915. PubMed id: 19594169 DOI: 10.1021/bi900084m
Date:
04-Dec-08     Release date:   18-Aug-09    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O16025  (AOSL_PLEHO) -  Allene oxide synthase-lipoxygenase protein
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1066 a.a.
684 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 2: E.C.1.13.11.40  - Arachidonate 8-lipoxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Arachidonate + O2 = (5Z,9E,11Z,14Z)-(8R)-8-hydroperoxyicosa-5,9,11,14- tetraenoate
Arachidonate
+ O(2)
= (5Z,9E,11Z,14Z)-(8R)-8-hydroperoxyicosa-5,9,11,14- tetraenoate
      Cofactor: Fe cation
   Enzyme class 3: E.C.4.2.1.92  - Hydroperoxide dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (9Z,11E,15Z)-(13S)-hydroperoxyoctadeca-9,11,15-trienoate = (9Z,15Z)- (13S)-12,13-epoxyoctadeca-9,11,15-trienoate + H2O
(9Z,11E,15Z)-(13S)-hydroperoxyoctadeca-9,11,15-trienoate
= (9Z,15Z)- (13S)-12,13-epoxyoctadeca-9,11,15-trienoate
+ H(2)O
      Cofactor: Heme-thiolate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen     3 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi900084m Biochemistry 48:7906-7915 (2009)
PubMed id: 19594169  
 
 
The 1.85 A structure of an 8R-lipoxygenase suggests a general model for lipoxygenase product specificity.
D.B.Neau, N.C.Gilbert, S.G.Bartlett, W.Boeglin, A.R.Brash, M.E.Newcomer.
 
  ABSTRACT  
 
Lipoxygenases (LOX) play pivotal roles in the biosynthesis of leukotrienes and other biologically active eicosanoids derived from arachidonic acid. A mechanistic understanding of substrate recognition, when lipoxygenases that recognize the same substrate generate different products, can be used to help guide the design of enzyme-specific inhibitors. We report here the 1.85 A resolution structure of an 8R-lipoxygenase from Plexaura homomalla, an enzyme with a sequence approximately 40% identical to that of human 5-LOX. The structure reveals a U-shaped channel, defined by invariant amino acids, that would allow substrate access to the catalytic iron. We demonstrate that mutations within the channel significantly impact enzyme activity and propose a novel model for substrate binding potentially applicable to other members of this enzyme family.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21345329 C.Palmieri-Thiers, J.C.Alberti, S.Canaan, V.Brunini, C.Gambotti, F.Tomi, E.H.Oliw, L.Berti, and J.Maury (2011).
Identification of putative residues involved in the accessibility of the substrate-binding site of lipoxygenase by site-directed mutagenesis studies.
  Arch Biochem Biophys, 509, 82-89.  
21257189 L.E.Chohany, K.A.Bishop, H.Camic, S.J.Sup, P.M.Findeis, and C.H.Clapp (2011).
Cationic substrates of soybean lipoxygenase-1.
  Bioorg Chem, 39, 94.  
21233389 N.C.Gilbert, S.G.Bartlett, M.T.Waight, D.B.Neau, W.E.Boeglin, A.R.Brash, and M.E.Newcomer (2011).
The structure of human 5-lipoxygenase.
  Science, 331, 217-219.
PDB code: 3o8y
20026599 R.Vogel, C.Jansen, J.Roffeis, P.Reddanna, P.Forsell, H.E.Claesson, H.Kuhn, and M.Walther (2010).
Applicability of the triad concept for the positional specificity of mammalian lipoxygenases.
  J Biol Chem, 285, 5369-5376.  
20946603 S.Bai, T.Du, and E.Khosravi (2010).
Applying internal coordinate mechanics to model the interactions between 8R-lipoxygenase and its substrate.
  BMC Bioinformatics, 11, S2.  
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.