PDBsum entry 1hb4

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Antibiotic biosynthesis PDB id
Protein chain
329 a.a. *
Waters ×357
* Residue conservation analysis
PDB id:
Name: Antibiotic biosynthesis
Title: Isopenicillin n synthase from aspergillus nidulans (oxygen exposed product from anaerobic acov fe complex)
Structure: Isopenicillin n synthase. Chain: a. Engineered: yes
Source: Emericella nidulans. Aspergillus nidulans. Organism_taxid: 162425. Strain: nm554. Plasmid: pjb703. Gene: pcb c. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.5Å     R-factor:   0.182     R-free:   0.199
Authors: J.M.Ogle,I.J.Clifton,P.J.Rutledge,J.M.Elkins,N.I.Burzlaff, R.M.Adlington,P.L.Roach,J.E.Baldwin
Key ref:
J.M.Ogle et al. (2001). Alternative oxidation by isopenicillin N synthase observed by X-ray diffraction. Chem Biol, 8, 1231-1237. PubMed id: 11755401 DOI: 10.1016/S1074-5521(01)00090-4
11-Apr-01     Release date:   23-Nov-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P05326  (IPNS_EMENI) -  Isopenicillin N synthase
331 a.a.
329 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 = SCV)
matches with 48.00% 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     biosynthetic process   5 terms 
  Biochemical function     oxidoreductase activity     7 terms  


    Added reference    
DOI no: 10.1016/S1074-5521(01)00090-4 Chem Biol 8:1231-1237 (2001)
PubMed id: 11755401  
Alternative oxidation by isopenicillin N synthase observed by X-ray diffraction.
J.M.Ogle, I.J.Clifton, P.J.Rutledge, J.M.Elkins, N.I.Burzlaff, R.M.Adlington, P.L.Roach, J.E.Baldwin.
BACKGROUND: Isopenicillin N synthase (IPNS) catalyses formation of bicyclic isopenicillin N, precursor to all penicillin and cephalosporin antibiotics, from the linear tripeptide delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine. IPNS is a non-haem iron(II)-dependent enzyme which utilises the full oxidising potential of molecular oxygen in catalysing the bicyclisation reaction. The reaction mechanism is believed to involve initial formation of the beta-lactam ring (via a thioaldehyde intermediate) to give an iron(IV)-oxo species, which then mediates closure of the 5-membered thiazolidine ring. RESULTS: Here we report experiments employing time-resolved crystallography to observe turnover of an isosteric substrate analogue designed to intercept the catalytic pathway at an early stage. Reaction in the crystalline enzyme-substrate complex was initiated by the application of high-pressure oxygen, and subsequent flash freezing allowed an oxygenated product to be trapped, bound at the iron centre. A mechanism for formation of the observed thiocarboxylate product is proposed. CONCLUSIONS: In the absence of its natural reaction partner (the N-H proton of the L-cysteinyl-D-valine amide bond), the proposed hydroperoxide intermediate appears to attack the putative thioaldehyde species directly. These results shed light on the events preceding beta-lactam closure in the IPNS reaction cycle, and enhance our understanding of the mechanism for reaction of the enzyme with its natural substrate.
  Selected figure(s)  
Figure 1.
Fig. 1. Mechanisms for the reaction of IPNS with ACV and ACOV. (a) Proposed mechanism for the reaction of IPNS with its natural substrate ACV [3]. (b) Proposed pathway for generation of the thiocarboxylate product from the substrate analogue ACOV. See text for details of compounds 1–10. AA, δ-( Image -α-aminoadipoyl).
Figure 4.
Fig. 4. Potential hydrogen bonding interactions in the active site region of the exposed IPNS:Fe(II):ACOV structure. The three exposed structures oriented to show the potential for hydrogen bonding around the thiocarboxylate oxygen, and to demonstrate the consistency of the thiocarboxylate electron density across the three structures. (a) From the 1.30 Å resolution structure in the plane of the thiocarboxylate, showing distances to Wat 402 and Wat 403. (b) The 1.30 Å 30 s, (c) the 1.40 Å 30 s, and (d) the 1.50 Å 120 s structures from an alternative angle.
  The above figures are reprinted by permission from Cell Press: Chem Biol (2001, 8, 1231-1237) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20078029 C.D.Brown-Marshall, A.R.Diebold, and E.I.Solomon (2010).
Reaction coordinate of isopenicillin N synthase: oxidase versus oxygenase activity.
  Biochemistry, 49, 1176-1182.  
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.  
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 code: 2vcm
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
17374503 J.M.Bollinger, and C.Krebs (2007).
Enzymatic C-H activation by metal-superoxo intermediates.
  Curr Opin Chem Biol, 11, 151-158.  
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
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.