PDBsum entry 1bk0

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B-lactam antibiotic PDB id
Jmol PyMol
Protein chain
329 a.a. *
Waters ×323
* Residue conservation analysis
PDB id:
Name: B-lactam antibiotic
Title: Isopenicillin n synthase from aspergillus nidulans (acv-fe complex)
Structure: Isopenicillin n synthase. Chain: a. Engineered: yes
Source: Emericella nidulans. Organism_taxid: 162425. Gene: pcb c. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.30Å     R-factor:   0.172     R-free:   0.190
Authors: P.L.Roach,I.J.Clifton,C.M.H.Hensgens,N.Shibata, C.J.Schofield,J.Hajdu,J.E.Baldwin
Key ref:
P.L.Roach et al. (1997). Structure of isopenicillin N synthase complexed with substrate and the mechanism of penicillin formation. Nature, 387, 827-830. PubMed id: 9194566 DOI: 10.1038/42990
14-Jul-98     Release date:   13-Jan-99    
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 = ACV)
corresponds exactly
+ 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: 10.1038/42990 Nature 387:827-830 (1997)
PubMed id: 9194566  
Structure of isopenicillin N synthase complexed with substrate and the mechanism of penicillin formation.
P.L.Roach, I.J.Clifton, C.M.Hensgens, N.Shibata, C.J.Schofield, J.Hajdu, J.E.Baldwin.
The biosynthesis of penicillin and cephalosporin antibiotics in microorganisms requires the formation of the bicyclic nucleus of penicillin. Isopenicillin N synthase (IPNS), a non-haem iron-dependent oxidase, catalyses the reaction of a tripeptide, delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine (ACV), and dioxygen to form isopenicillin N and two water molecules. Mechanistic studies suggest the reaction is initiated by ligation of the substrate thiolate to the iron centre, and proceeds through an enzyme-bound monocyclic intermediate. Here we report the crystal structure of IPNS complexed to ferrous iron and ACV, determined to 1.3 A resolution. Based on the structure, we propose a mechanism for penicillin formation that involves ligation of ACV to the iron centre, creating a vacant iron coordination site into which dioxygen can bind. Subsequently, iron-dioxygen and iron-oxo species remove the requisite hydrogens from ACV without the direct assistance of protein residues. The crystal structure of the complex with the dioxygen analogue, NO and ACV bound to the active-site iron supports this hypothesis.
  Selected figure(s)  
Figure 2.
Figure 2 Mechanism for isopenicillin N formation and the formation of the Fe: ACV: NO:. sp;IPNS complex.
Figure 3.
Figure 3 Comparison of the structures of Mn: IPNS (a) and Fe(II): ACV: IPNS (. b) from the same orientation. The jelly-roll motif is in green, the C-terminal region (residues 313-331) cyan, the active-site metal ion (manganese in a, iron in b) orange, the key substrate-binding residues (His 214, His 270, Asp 216, Arg 87, Arg 279, Tyr 189 and Ser 281) magenta, and the ACV yellow.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1997, 387, 827-830) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

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PDB codes: 2vcm 2ve1
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PDB codes: 1w3v 1w3x
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Purification, crystallization and preliminary X-ray diffraction of Cys103Ala acyl coenzyme A: isopenicillin N acyltransferase from Penicillium chrysogenum.
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Unraveling the substrate-metal binding site of ferrochelatase: an X-ray absorption spectroscopic study.
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Structural genomics: a pipeline for providing structures for the biologist.
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PDB code: 1jr7
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Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene.
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Structure of proline 3-hydroxylase. Evolution of the family of 2-oxoglutarate dependent oxygenases.
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PDB codes: 1e5r 1e5s
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Purification, crystallization and preliminary X-ray diffraction of anthocyanidin synthase from Arabidopsis thaliana.
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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.
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PDB codes: 1hb1 1hb2 1hb3 1hb4
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Kinetic mechanism of the beta-lactam synthetase of Streptomyces clavuligerus.
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Site-directed mutagenesis of 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase. Identification of residues involved in metallocenter formation and substrate binding.
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Isopenicillin N Synthase: An Enzyme at Work.
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PDB code: 1ndo
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PDB code: 3pcd
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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.