PDBsum entry 1qiq

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Antibiotic biosynthesis PDB id
Jmol PyMol
Protein chain
328 a.a. *
Waters ×410
* Residue conservation analysis
PDB id:
Name: Antibiotic biosynthesis
Title: Isopenicillin n synthase from aspergillus nidulans (acmc fe complex)
Structure: Isopenicillin n synthase. Chain: a. Engineered: yes
Source: Emericella nidulans. Organism_taxid: 162425. Strain: nm554. Plasmid: pjb703. Gene: pcb c. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.50Å     R-factor:   0.173     R-free:   0.199
Authors: P.J.Rutledge,I.J.Clifton,N.I.Burzlaff,P.L.Roach, R.M.Adlington,J.E.Baldwin
Key ref:
N.I.Burzlaff et al. (1999). The reaction cycle of isopenicillin N synthase observed by X-ray diffraction. Nature, 401, 721-724. PubMed id: 10537113 DOI: 10.1038/44400
15-Jun-99     Release date:   16-Jun-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P05326  (IPNS_EMENI) -  Isopenicillin N synthase
331 a.a.
328 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Isopenicillin-N synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Penicillin N and Deacetoxycephalosporin C Biosynthesis
      Reaction: N-((5S)-5-amino-5-carboxypentanoyl)-L-cysteinyl-D-valine + O2 = isopenicillin N + 2 H2O
+ O(2)
isopenicillin N
Bound ligand (Het Group name = ACC)
matches with 84.00% similarity
+ 2 × H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cellular_component   1 term 
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     4 terms  


    Added reference    
DOI no: 10.1038/44400 Nature 401:721-724 (1999)
PubMed id: 10537113  
The reaction cycle of isopenicillin N synthase observed by X-ray diffraction.
N.I.Burzlaff, P.J.Rutledge, I.J.Clifton, C.M.Hensgens, M.Pickford, R.M.Adlington, P.L.Roach, J.E.Baldwin.
Isopenicillin N synthase (IPNS), a non-haem iron-dependent oxidase, catalyses the biosynthesis of isopenicillin N (IPN), the precursor of all penicillins and cephalosporins. The key steps in this reaction are the two iron-dioxygen-mediated ring closures of the tripeptide delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine (ACV). It has been proposed that the four-membered beta-lactam ring forms initially, associated with a highly oxidized iron(iv)-oxo (ferryl) moiety, which subsequently mediates closure of the five-membered thiazolidine ring. Here we describe observation of the IPNS reaction in crystals by X-ray crystallography. IPNS Fe2+ substrate crystals were grown anaerobically, exposed to high pressures of oxygen to promote reaction and frozen, and their structures were elucidated by X-ray diffraction. Using the natural substrate ACV, this resulted in the IPNS x Fe2+ x IPN product complex. With the substrate analogue, delta-(L-alpha-aminoadipoyl)-L-cysteinyl-L-S-methylcysteine (ACmC) in the crystal, the reaction cycle was interrupted at the monocyclic stage. These mono- and bicyclic structures support our hypothesis of a two-stage reaction sequence leading to penicillin. Furthermore, the formation of a monocyclic sulphoxide product from ACmC is most simply explained by the interception of a high-valency iron-oxo species.
  Selected figure(s)  
Figure 2.
Figure 2 Proposed mechanisms for the oxidation of ACV and ACmC to bicyclic and monocyclic products, respectively. See text for details of compounds 1-6. AA, L- -( -aminoadipoyl).
Figure 3.
Figure 3 Stereo views of the two substrates and two products overlaid. The key regions that participate in the reaction and the iron atom (orange) are shown; the aminoadipoyl side chain, which does not move significantly, is omitted for clarity. Shown are ACV (white), IPN (yellow), ACmC (blue) and its monocyclic sulphoxide product (pink). Figures were prepared using the programs MOLSCRIPT20 and Raster3D (ref. 21).
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1999, 401, 721-724) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21505498 P.K.Sydor, S.M.Barry, O.M.Odulate, F.Barona-Gomez, S.W.Haynes, C.Corre, L.Song, and G.L.Challis (2011).
Regio- and stereodivergent antibiotic oxidative carbocyclizations catalysed by Rieske oxygenase-like enzymes.
  Nat Chem, 3, 388-392.  
21088787 W.A.Schenk (2011).
The coordination chemistry of small sulfur-containing molecules: a personal perspective.
  Dalton Trans, 40, 1209-1219.  
20218986 A.Benjdia, S.Subramanian, J.Leprince, H.Vaudry, M.K.Johnson, and O.Berteau (2010).
Anaerobic sulfatase-maturating enzyme--a mechanistic link with glycyl radical-activating enzymes?
  FEBS J, 277, 1906-1920.  
21068844 C.Yi, G.Jia, G.Hou, Q.Dai, W.Zhang, G.Zheng, X.Jian, C.G.Yang, Q.Cui, and C.He (2010).
Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase.
  Nature, 468, 330-333.
PDB codes: 3o1m 3o1o 3o1p 3o1r 3o1s 3o1t 3o1u 3o1v
20237680 V.J.Dungan, Y.Ortin, H.Mueller-Bunz, and P.J.Rutledge (2010).
Design and synthesis of a tetradentate '3-amine-1-carboxylate' ligand to mimic the metal binding environment at the non-heme iron(II) oxidase active site.
  Org Biomol Chem, 8, 1666-1673.  
19520834 B.Sjöblom, M.Polentarutti, and K.Djinovic-Carugo (2009).
Structural study of X-ray induced activation of carbonic anhydrase.
  Proc Natl Acad Sci U S A, 106, 10609-10613.
PDB codes: 2vva 2vvb
19444009 K.Morokuma (2009).
Theoretical studies of structure, function and reactivity of molecules-A personal account.
  Proc Jpn Acad Ser B Phys Biol Sci, 85, 167-182.  
19516340 R.M.Cicchillo, H.Zhang, J.A.Blodgett, J.T.Whitteck, G.Li, S.K.Nair, W.A.van der Donk, and W.W.Metcalf (2009).
An unusual carbon-carbon bond cleavage reaction during phosphinothricin biosynthesis.
  Nature, 459, 871-874.
PDB code: 3g7d
19598184 W.Ge, I.J.Clifton, A.R.Howard-Jones, J.E.Stok, R.M.Adlington, J.E.Baldwin, and P.J.Rutledge (2009).
Structural studies on the reaction of isopenicillin N synthase with a sterically demanding depsipeptide substrate analogue.
  Chembiochem, 10, 2025-2031.
PDB codes: 2vcm 2ve1
19489722 W.W.Metcalf, and W.A.van der Donk (2009).
Biosynthesis of phosphonic and phosphinic acid natural products.
  Annu Rev Biochem, 78, 65-94.  
17981760 A.Siddiq, L.R.Aminova, and R.R.Ratan (2008).
Prolyl 4-hydroxylase activity-responsive transcription factors: from hydroxylation to gene expression and neuroprotection.
  Front Biosci, 13, 2875-2887.  
18838806 K.Watanabe (2008).
Exploring the biosynthesis of natural products and their inherent suitability for the rational design of desirable compounds through genetic engineering.
  Biosci Biotechnol Biochem, 72, 2491-2506.  
18366686 L.Gidijala, R.A.Bovenberg, P.Klaassen, I.J.van der Klei, M.Veenhuis, and J.A.Kiel (2008).
Production of functionally active Penicillium chrysogenum isopenicillin N synthase in the yeast Hansenula polymorpha.
  BMC Biotechnol, 8, 29.  
19020684 P.C.Bruijnincx, G.van Koten, and R.J.Klein Gebbink (2008).
Mononuclear non-heme iron enzymes with the 2-His-1-carboxylate facial triad: recent developments in enzymology and modeling studies.
  Chem Soc Rev, 37, 2716-2744.  
17907118 A.C.Stewart, I.J.Clifton, R.M.Adlington, J.E.Baldwin, and P.J.Rutledge (2007).
A cyclobutanone analogue mimics penicillin in binding to isopenicillin N synthase.
  Chembiochem, 8, 2003-2007.
PDB code: 2jb4
17301803 A.Ozer, and R.K.Bruick (2007).
Non-heme dioxygenases: cellular sensors and regulators jelly rolled into one?
  Nat Chem Biol, 3, 144-153.  
17390002 D.Hoffmeister, and N.P.Keller (2007).
Natural products of filamentous fungi: enzymes, genes, and their regulation.
  Nat Prod Rep, 24, 393-416.  
17220900 D.P.Galonić, E.W.Barr, C.T.Walsh, J.M.Bollinger, and C.Krebs (2007).
Two interconverting Fe(IV) intermediates in aliphatic chlorination by the halogenase CytC3.
  Nat Chem Biol, 3, 113-116.  
16444759 A.Daruzzaman, I.J.Clifton, R.M.Adlington, J.E.Baldwin, and P.J.Rutledge (2006).
Unexpected oxidation of a depsipeptide substrate analogue in crystalline isopenicillin N synthase.
  Chembiochem, 7, 351-358.
PDB codes: 1w3v 1w3x
16113715 N.J.Kershaw, M.E.Caines, M.C.Sleeman, and C.J.Schofield (2005).
The enzymology of clavam and carbapenem biosynthesis.
  Chem Commun (Camb), (), 4251-4263.  
14718929 K.Valegård, A.C.Terwisscha van Scheltinga, A.Dubus, G.Ranghino, L.M.Oster, J.Hajdu, and I.Andersson (2004).
The structural basis of cephalosporin formation in a mononuclear ferrous enzyme.
  Nat Struct Mol Biol, 11, 95.
PDB codes: 1unb 1uo9 1uob 1uof 1uog
12611886 I.J.Clifton, L.X.Doan, M.C.Sleeman, M.Topf, H.Suzuki, R.C.Wilmouth, and C.J.Schofield (2003).
Crystal structure of carbapenem synthase (CarC).
  J Biol Chem, 278, 20843-20850.
PDB codes: 1nx4 1nx8
11914506 C.M.Hensgens, E.A.Kroezinga, B.A.van Montfort, J.M.van der Laan, J.D.Sutherland, and B.W.Dijkstra (2002).
Purification, crystallization and preliminary X-ray diffraction of Cys103Ala acyl coenzyme A: isopenicillin N acyltransferase from Penicillium chrysogenum.
  Acta Crystallogr D Biol Crystallogr, 58, 716-718.  
12039004 M.J.Ryle, and R.P.Hausinger (2002).
Non-heme iron oxygenases.
  Curr Opin Chem Biol, 6, 193-201.  
11514230 A.M.Cerdeño, M.J.Bibb, and G.L.Challis (2001).
Analysis of the prodiginine biosynthesis gene cluster of Streptomyces coelicolor A3(2): new mechanisms for chain initiation and termination in modular multienzymes.
  Chem Biol, 8, 817-829.  
11755401 J.M.Ogle, I.J.Clifton, P.J.Rutledge, J.M.Elkins, N.I.Burzlaff, R.M.Adlington, P.L.Roach, and J.E.Baldwin (2001).
Alternative oxidation by isopenicillin N synthase observed by X-ray diffraction.
  Chem Biol, 8, 1231-1237.
PDB codes: 1hb1 1hb2 1hb3 1hb4
10985764 B.O.Bachmann, and C.A.Townsend (2000).
Kinetic mechanism of the beta-lactam synthetase of Streptomyces clavuligerus.
  Biochemistry, 39, 11187-11193.  
10679381 G.A.Petsko, and D.Ringe (2000).
Observation of unstable species in enzyme-catalyzed transformations using protein crystallography.
  Curr Opin Chem Biol, 4, 89-94.  
11114513 I.Schlichting, and K.Chu (2000).
Trapping intermediates in the crystal: ligand binding to myoglobin.
  Curr Opin Struct Biol, 10, 744-752.  
11091371 W.A.Schenk (2000).
Isopenicillin N Synthase: An Enzyme at Work.
  Angew Chem Int Ed Engl, 39, 3409-3411.  
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 codes are shown on the right.