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PDBsum entry 1afr

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protein metals Protein-protein interface(s) links
Oxidoreductase PDB id
1afr
Jmol
Contents
Protein chains
(+ 0 more) 345 a.a. *
Metals
FE2 ×12
Waters ×538
* Residue conservation analysis
PDB id:
1afr
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)
Resolution:
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
Date:
13-Mar-97     Release date:   15-May-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Enzyme reactions 
   Enzyme class: E.C.1.14.19.2  - Acyl-[acyl-carrier-protein] desaturase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Stearoyl-[acyl-carrier-protein] + reduced acceptor + O2 = oleoyl-[acyl- carrier-protein] + acceptor + 2 H2O
Stearoyl-[acyl-carrier-protein]
+ 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  

 

 
    reference    
 
 
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.
 
  ABSTRACT  
 
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

  PubMed id Reference
21267492 M.Högbom (2011).
Metal use in ribonucleotide reductase R2, di-iron, di-manganese and heterodinuclear--an intricate bioinorganic workaround to use different metals for the same reaction.
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A Mycobacterium tuberculosis ligand-binding Mn/Fe protein reveals a new cofactor in a remodeled R2-protein scaffold.
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PDB code: 3ee4
19173070 J.M.Bollinger, Y.Diao, M.L.Matthews, G.Xing, and C.Krebs (2009).
myo-Inositol oxygenase: a radical new pathway for O(2) and C-H activation at a nonheme diiron cluster.
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19363032 J.Shanklin, J.E.Guy, G.Mishra, and Y.Lindqvist (2009).
Desaturases: Emerging Models for Understanding Functional Diversification of Diiron-containing Enzymes.
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19088315 R.E.Minto, B.J.Blacklock, H.Younus, and A.C.Pratt (2009).
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PDB codes: 2ibn 3bxd
18811130 A.T.Fiedler, X.Shan, M.P.Mehn, J.Kaizer, S.Torelli, J.R.Frisch, M.Kodera, and L.Que (2008).
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18796606 E.J.Whittle, A.E.Tremblay, P.H.Buist, and J.Shanklin (2008).
Revealing the catalytic potential of an acyl-ACP desaturase: tandem selective oxidation of saturated fatty acids.
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18576633 J.K.Schwartz, X.S.Liu, T.Tosha, E.C.Theil, and E.I.Solomon (2008).
Spectroscopic definition of the ferroxidase site in M ferritin: comparison of binuclear substrate vs cofactor active sites.
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18599072 Q.Xu, A.A.Canutescu, G.Wang, M.Shapovalov, Z.Obradovic, and R.L.Dunbrack (2008).
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18387369 R.E.Minto, and B.J.Blacklock (2008).
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19030627 S.Das, J.Bhattacharyya, and S.Mukhopadhyay (2008).
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19915653 S.Friedle, J.J.Kodanko, K.L.Fornace, and S.J.Lippard (2008).
9-Triptycenecarboxylate-Bridged Diiron(II) Complexes: Capture of the Paddlewheel Geometric Isomer.
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19011101 T.Tosha, M.R.Hasan, and E.C.Theil (2008).
The ferritin Fe2 site at the diiron catalytic center controls the reaction with O2 in the rapid mineralization pathway.
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18256868 Y.Li, M.Dietrich, R.D.Schmid, B.He, P.Ouyang, and V.B.Urlacher (2008).
Identification and functional expression of a Delta9-fatty acid desaturase from Psychrobacter urativorans in Escherichia coli.
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18458342 Y.S.Choi, H.Zhang, J.S.Brunzelle, S.K.Nair, and H.Zhao (2008).
In vitro reconstitution and crystal structure of p-aminobenzoate N-oxygenase (AurF) involved in aureothin biosynthesis.
  Proc Natl Acad Sci U S A, 105, 6858-6863.
PDB codes: 3chh 3chi 3cht 3chu
17406726 A.E.Tremblay, E.Whittle, P.H.Buist, and J.Shanklin (2007).
Stereochemistry of Delta4 dehydrogenation catalyzed by an ivy (Hedera helix) Delta9 desaturase homolog.
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17072561 A.Kachroo, J.Shanklin, E.Whittle, L.Lapchyk, D.Hildebrand, and P.Kachroo (2007).
The Arabidopsis stearoyl-acyl carrier protein-desaturase family and the contribution of leaf isoforms to oleic acid synthesis.
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17679698 C.Mathevon, F.Pierrel, J.L.Oddou, R.Garcia-Serres, G.Blondin, J.M.Latour, S.Ménage, S.Gambarelli, M.Fontecave, and M.Atta (2007).
tRNA-modifying MiaE protein from Salmonella typhimurium is a nonheme diiron monooxygenase.
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The crystal structure of the ivy Delta4-16:0-ACP desaturase reveals structural details of the oxidized active site and potential determinants of regioselectivity.
  J Biol Chem, 282, 19863-19871.
PDB code: 2uw1
17584793 K.A.Feenstra, W.Pirovano, K.Krab, and J.Heringa (2007).
Sequence harmony: detecting functional specificity from alignments.
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Dioxygen activation at non-heme diiron centers: oxidation of a proximal residue in the I100W variant of toluene/o-xylene monooxygenase hydroxylase.
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PDB code: 2rdb
17967027 L.J.Murray, S.G.Naik, D.O.Ortillo, R.García-Serres, J.K.Lee, B.H.Huynh, and S.J.Lippard (2007).
Characterization of the arene-oxidizing intermediate in ToMOH as a diiron(III) species.
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A small membrane-peripheral region close to the active center determines regioselectivity of membrane-bound fatty acid desaturases from Aspergillus nidulans.
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Synthesis, characterization, and preliminary oxygenation studies of benzyl- and ethyl-substituted pyridine ligands of carboxylate-rich diiron(II) complexes.
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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.
  Biochemistry, 45, 5217-5227.
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.
  Proc Natl Acad Sci U S A, 103, 17220-17224.
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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17176061 M.H.Sazinsky, P.W.Dunten, M.S.McCormick, A.DiDonato, and S.J.Lippard (2006).
X-ray structure of a hydroxylase-regulatory protein complex from a hydrocarbon-oxidizing multicomponent monooxygenase, Pseudomonas sp. OX1 phenol hydroxylase.
  Biochemistry, 45, 15392-15404.
PDB codes: 2inn 2inp
16927313 M.Simurdiak, J.Lee, and H.Zhao (2006).
A new class of arylamine oxygenases: evidence that p-aminobenzoate N-oxygenase (AurF) is a di-iron enzyme and further mechanistic studies.
  Chembiochem, 7, 1169-1172.  
17012379 P.M.Brown, T.T.Caradoc-Davies, J.M.Dickson, G.J.Cooper, K.M.Loomes, and E.N.Baker (2006).
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
16605252 P.Sobrado, K.S.Lyle, S.P.Kaul, M.M.Turco, I.Arabshahi, A.Marwah, and B.G.Fox (2006).
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.
  Biochemistry, 45, 4848-4858.  
16813407 S.Yoon, and S.J.Lippard (2006).
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.  
15929999 D.H.Dyer, K.S.Lyle, I.Rayment, and B.G.Fox (2005).
X-ray structure of putative acyl-ACP desaturase DesA2 from Mycobacterium tuberculosis H37Rv.
  Protein Sci, 14, 1508-1517.
PDB code: 1za0
15939740 E.Whittle, E.B.Cahoon, S.Subrahmanyam, and J.Shanklin (2005).
A multifunctional acyl-acyl carrier protein desaturase from Hedera helix L. (English ivy) can synthesize 16- and 18-carbon monoene and diene products.
  J Biol Chem, 280, 28169-28176.  
16289312 F.Bouvier, A.Rahier, and B.Camara (2005).
Biogenesis, molecular regulation and function of plant isoprenoids.
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15700297 J.R.Calhoun, F.Nastri, O.Maglio, V.Pavone, A.Lombardi, and W.F.DeGrado (2005).
Artificial diiron proteins: from structure to function.
  Biopolymers, 80, 264-278.  
15711796 M.C.Mansilla, and D.de Mendoza (2005).
The Bacillus subtilis desaturase: a model to understand phospholipid modification and temperature sensing.
  Arch Microbiol, 183, 229-235.  
15727041 R.J.Wilson (2005).
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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15166287 X.Liu, and E.C.Theil (2004).
Ferritin reactions: direct identification of the site for the diferric peroxide reaction intermediate.
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14567684 K.R.Strand, Y.S.Yang, K.K.Andersson, and E.I.Solomon (2003).
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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12704186 M.Moche, J.Shanklin, A.Ghoshal, and Y.Lindqvist (2003).
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.
  J Biol Chem, 278, 25072-25080.
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.
  Proc Natl Acad Sci U S A, 100, 3772-3777.
PDB code: 1nvo
12730185 S.G.Altabe, P.Aguilar, G.M.Caballero, and D.de 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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12324476 A.R.Diaz, M.C.Mansilla, A.J.Vila, and D.de Mendoza (2002).
Membrane topology of the acyl-lipid desaturase from Bacillus subtilis.
  J Biol Chem, 277, 48099-48106.  
12413540 B.Behrouzian, and P.H.Buist (2002).
Fatty acid desaturation: variations on an oxidative theme.
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12354110 B.J.Blacklock, and J.G.Jaworski (2002).
Studies into factors contributing to substrate specificity of membrane-bound 3-ketoacyl-CoA synthases.
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12203571 C.Beckmann, J.Rattke, N.J.Oldham, P.Sperling, E.Heinz, and W.Boland (2002).
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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12146979 C.E.Rogge, and B.G.Fox (2002).
Desaturation, chain scission, and register-shift of oxygen-substituted fatty acids during reaction with stearoyl-ACP desaturase.
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12186554 E.Cadieux, V.Vrajmasu, C.Achim, J.Powlowski, and E.Münck (2002).
Biochemical, Mössbauer, and EPR studies of the diiron cluster of phenol hydroxylase from Pseudomonas sp. strain CF 600.
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Noncovalent self-assembly of a heterotetrameric diiron protein.
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12217522 J.G.Wallis, J.L.Watts, and J.Browse (2002).
Polyunsaturated fatty acid synthesis: what will they think of next?
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Proton and metal ion-dependent assembly of a model diiron protein.
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Dioxygen Activation and Methane Hydroxylation by Soluble Methane Monooxygenase: A Tale of Two Irons and Three Proteins A list of abbreviations can be found in Section 7.
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10841536 A.Lombardi, C.M.Summa, S.Geremia, L.Randaccio, V.Pavone, and W.F.DeGrado (2000).
Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins.
  Proc Natl Acad Sci U S A, 97, 6298-6305.
PDB code: 1ec5
11027301 E.B.Cahoon, and J.Shanklin (2000).
Substrate-dependent mutant complementation to select fatty acid desaturase variants for metabolic engineering of plant seed oils.
  Proc Natl Acad Sci U S A, 97, 12350-12355.  
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Threonine 201 in the diiron enzyme toluene 4-monooxygenase is not required for catalysis.
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Exploring the possibilities presented by protein engineering.
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Resonance Raman studies of the stoichiometric catalytic turnover of a substrate-stearoyl-acyl carrier protein delta(9) desaturase complex.
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Tertiary templates for the design of diiron proteins.
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Production of novel oils in plants.
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Biosynthesis of fatty acids and related metabolites.
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Recent advances in the biochemistry and molecular biology of fatty acyl desaturases.
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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.
  Biochemistry, 37, 10798-10807.
PDB code: 1biq
9778341 J.A.Broadwater, J.Ai, T.M.Loehr, J.Sanders-Loehr, and B.G.Fox (1998).
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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DESATURATION AND RELATED MODIFICATIONS OF FATTY ACIDS1.
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Harnessing free radicals: formation and function of the tyrosyl radical in ribonucleotide reductase.
  Trends Biochem Sci, 23, 438-443.  
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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
9812895 P.Broun, J.Shanklin, E.Whittle, and C.Somerville (1998).
Catalytic plasticity of fatty acid modification enzymes underlying chemical diversity of plant lipids.
  Science, 282, 1315-1317.  
9454605 S.E.Parkin, S.Chen, B.A.Ley, L.Mangravite, D.E.Edmondson, B.H.Huynh, and J.M.Bollinger (1998).
Electron injection through a specific pathway determines the outcome of oxygen activation at the diiron cluster in the F208Y mutant of Escherichia coli ribonucleotide reductase protein R2.
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9914255 U.Ermler, W.Grabarse, S.Shima, M.Goubeaud, and R.K.Thauer (1998).
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