PDBsum entry 1afr

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
Protein chains
(+ 0 more) 345 a.a. *
FE2 ×12
Waters ×538
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Stearoyl-acyl carrier protein desaturase from castor seeds
Structure: Delta9 stearoyl-acyl carrier protein desaturase. Chain: a, b, c, d, e, f. Synonym: fatty acid desaturase. Engineered: yes
Source: Ricinus communis. Castor bean. Organism_taxid: 3988. Organ: seed. Tissue: seeds. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
2.40Å     R-factor:   0.220     R-free:   0.285
Authors: Y.Lindqvist,W.Huang,G.Schneider
Key ref: Y.Lindqvist et al. (1996). Crystal structure of delta9 stearoyl-acyl carrier protein desaturase from castor seed and its relationship to other di-iron proteins. EMBO J, 15, 4081-4092. PubMed id: 8861937
13-Mar-97     Release date:   15-May-97    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P22337  (STAD_RICCO) -  Acyl-[acyl-carrier-protein] desaturase, chloroplastic
396 a.a.
345 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Acyl-[acyl-carrier-protein] desaturase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Stearoyl-[acyl-carrier-protein] + reduced acceptor + O2 = oleoyl-[acyl- carrier-protein] + acceptor + 2 H2O
+ reduced acceptor
+ O(2)
= oleoyl-[acyl- carrier-protein]
+ acceptor
+ 2 × H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     2 terms  


EMBO J 15:4081-4092 (1996)
PubMed id: 8861937  
Crystal structure of delta9 stearoyl-acyl carrier protein desaturase from castor seed and its relationship to other di-iron proteins.
Y.Lindqvist, W.Huang, G.Schneider, J.Shanklin.
The three-dimensional structure of recombinant homodimeric delta9 stearoyl-acyl carrier protein desaturase, the archetype of the soluble plant fatty acid desaturases that convert saturated to unsaturated fatty acids, has been determined by protein crystallographic methods to a resolution of 2.4 angstroms. The structure was solved by a combination of single isomorphous replacement, anomalous contribution from the iron atoms to the native diffraction data and 6-fold non-crystallographic symmetry averaging. The 363 amino acid monomer consists of a single domain of 11 alpha-helices. Nine of these form an antiparallel helix bundle. The enzyme subunit contains a di-iron centre, with ligands from four of the alpha-helices in the helix bundle. The iron ions are bound in a highly symmetric environment, with one of the irons forming interactions with the side chains of E196 and H232 and the second iron with the side chains of E105 and H146. Two additional glutamic acid side chains, from E143 and E229, are within coordination distance to both iron ions. A water molecule is found within the second coordination sphere from the iron atoms. The lack of electron density corresponding to a mu-oxo bridge, and the long (4.2 angstroms) distance between the iron ions suggests that this probably represents the diferrous form of the enzyme. A deep channel which probably binds the fatty acid extends from the surface into the interior of the enzyme. Modelling of the substrate, stearic acid, into this channel places the delta9 carbon atom in the vicinity of one of the iron ions.

Literature references that cite this PDB file's key reference

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PDB code: 3ee4
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PDB codes: 2ibn 3bxd
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PDB codes: 3chh 3chi 3cht 3chu
17406726 A.E.Tremblay, E.Whittle, P.H.Buist, and J.Shanklin (2007).
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PDB code: 2uw1
17584793 K.A.Feenstra, W.Pirovano, K.Krab, and J.Heringa (2007).
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PDB code: 2rdb
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16618110 G.A.Zornetzer, B.G.Fox, and J.L.Markley (2006).
Solution structures of spinach acyl carrier protein with decanoate and stearate.
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PDB codes: 2ava 2fva 2fve 2fvf
16819737 H.Wade, S.E.Stayrook, and W.F.Degrado (2006).
The structure of a designed diiron(III) protein: implications for cofactor stabilization and catalysis.
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17088542 J.E.Guy, I.A.Abreu, M.Moche, Y.Lindqvist, E.Whittle, and J.Shanklin (2006).
A single mutation in the castor Delta9-18:0-desaturase changes reaction partitioning from desaturation to oxidase chemistry.
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PDB code: 2j2f
16642305 L.Tong, P.Shu-Ming, D.Wu-Yuan, M.Dan-Wei, X.Ying, X.Meng, and C.Fang (2006).
Characterization of a new stearoyl-acyl carrier protein desaturase gene from Jatropha curcas.
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X-ray structure of a hydroxylase-regulatory protein complex from a hydrocarbon-oxidizing multicomponent monooxygenase, Pseudomonas sp. OX1 phenol hydroxylase.
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PDB codes: 2inn 2inp
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A new class of arylamine oxygenases: evidence that p-aminobenzoate N-oxygenase (AurF) is a di-iron enzyme and further mechanistic studies.
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Crystal structure of a substrate complex of myo-inositol oxygenase, a di-iron oxygenase with a key role in inositol metabolism.
  Proc Natl Acad Sci U S A, 103, 15032-15037.
PDB code: 2huo
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Identification of the binding region of the [2Fe-2S] ferredoxin in stearoyl-acyl carrier protein desaturase: insight into the catalytic complex and mechanism of action.
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Mechanistic studies of the oxidative N-dealkylation of a substrate tethered to carboxylate-bridged diiron(II) complexes, [Fe2(mu-O2CAr(Tol))2(O2CAr(Tol))2(N,N-Bn2en)2].
  Inorg Chem, 45, 5438-5446.  
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X-ray structure of putative acyl-ACP desaturase DesA2 from Mycobacterium tuberculosis H37Rv.
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PDB code: 1za0
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A multifunctional acyl-acyl carrier protein desaturase from Hedera helix L. (English ivy) can synthesize 16- and 18-carbon monoene and diene products.
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16289312 F.Bouvier, A.Rahier, and B.Camara (2005).
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Artificial diiron proteins: from structure to function.
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15711796 M.C.Mansilla, and Mendoza (2005).
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Parasite plastids: approaching the endgame.
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Mechanistic studies on oxidation of hydrazine by a mu-oxo diiron(III,III) complex in aqueous acidic media-proton coupled electron transfer.
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Circular dichroism and magnetic circular dichroism studies of the biferrous form of the R2 subunit of ribonucleotide reductase from mouse: comparison to the R2 from Escherichia coli and other binuclear ferrous enzymes.
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Azide and acetate complexes plus two iron-depleted crystal structures of the di-iron enzyme delta9 stearoyl-acyl carrier protein desaturase. Implications for oxygen activation and catalytic intermediates.
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PDB codes: 1oq4 1oq7 1oq9 1oqb
12655072 O.Maglio, F.Nastri, V.Pavone, A.Lombardi, and W.F.DeGrado (2003).
Preorganization of molecular binding sites in designed diiron proteins.
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PDB code: 1nvo
12730185 S.G.Altabe, P.Aguilar, G.M.Caballero, and Mendoza (2003).
The Bacillus subtilis acyl lipid desaturase is a delta5 desaturase.
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12730190 T.J.Stillman, P.P.Connolly, C.L.Latimer, A.F.Morland, M.A.Quail, S.C.Andrews, A.Treffry, J.R.Guest, P.J.Artymiuk, and P.M.Harrison (2003).
Insights into the effects on metal binding of the systematic substitution of five key glutamate ligands in the ferritin of Escherichia coli.
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12413540 B.Behrouzian, and P.H.Buist (2002).
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Characterization of a Delta8-sphingolipid desaturase from higher plants: a stereochemical and mechanistic study on the origin of E,Z isomers.
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Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins.
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PDB code: 1ec5
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Substrate-dependent mutant complementation to select fatty acid desaturase variants for metabolic engineering of plant seed oils.
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Tertiary templates for the design of diiron proteins.
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Crystal structures of two self-hydroxylating ribonucleotide reductase protein R2 mutants: structural basis for the oxygen-insertion step of hydroxylation reactions catalyzed by diiron proteins.
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PDB code: 1biq
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Peroxodiferric intermediate of stearoyl-acyl carrier protein delta 9 desaturase: oxidase reactivity during single turnover and implications for the mechanism of desaturation.
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Structure of Salmonella typhimurium nrdF ribonucleotide reductase in its oxidized and reduced forms.
  Biochemistry, 37, 13359-13369.
PDB codes: 1r2f 2r2f
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Catalytic plasticity of fatty acid modification enzymes underlying chemical diversity of plant lipids.
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Oxygen activating nonheme iron enzymes.
  Curr Opin Chem Biol, 2, 159-172.  
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Biochemical characterization of a delta12 acyl-lipid desaturase after overexpression of the enzyme in Escherichia coli.
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