PDBsum entry 1ips

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Antibiotic biosynthesis PDB id
Jmol PyMol
Protein chains
328 a.a. *
_MN ×4
Waters ×194
* Residue conservation analysis
PDB id:
Name: Antibiotic biosynthesis
Title: Isopenicillin n synthase from aspergillus nidulans (manganese complex)
Structure: Isopenicillin n synthase. Chain: a, b. Engineered: yes
Source: Emericella nidulans. Organism_taxid: 162425. Gene: pcb c. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Monomer (from PDB file)
2.50Å     R-factor:   0.220     R-free:   0.265
Authors: P.L.Roach,I.J.Clifton,V.Fulop,K.Harlos,G.J.Barton,J.Hajdu, I.Andersson,C.J.Schofield,J.E.Baldwin
Key ref: P.L.Roach et al. (1995). Crystal structure of isopenicillin N synthase is the first from a new structural family of enzymes. Nature, 375, 700-704. PubMed id: 7791906
21-Mar-97     Release date:   25-Mar-98    
Go to PROCHECK summary

Protein chains
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
+ 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    
Nature 375:700-704 (1995)
PubMed id: 7791906  
Crystal structure of isopenicillin N synthase is the first from a new structural family of enzymes.
P.L.Roach, I.J.Clifton, V.Fülöp, K.Harlos, G.J.Barton, J.Hajdu, I.Andersson, C.J.Schofield, J.E.Baldwin.
Penicillin antibiotics are all produced from fermentation-derived penicillins because their chemical synthesis is not commercially viable. The key step in penicillin biosynthesis, in which both the beta-lactam and thiazolidine rings of the nucleus are created, is mediated by isopenicillin N synthase (IPNS), which binds ferrous iron and uses dioxygen as a cosubstrate. In a unique enzymatic step, with no chemical precedent, IPNS catalyses the transfer of four hydrogen atoms from its tripeptide substrate to dioxygen forming, in a single reaction, the complete bicyclic nucleus of the penicillins. We now report the structure of IPNS complexed with manganese, which reveals the active site is unusually buried within a 'jelly-roll' motif and lined by hydrophobic residues, and suggest how this structure permits the process of penicillin formation. Sequence analyses indicate IPNS, 1-aminocyclopropane-1-carboxylic acid oxidase and many of the 2-oxo-acid-dependent oxygenases contain a conserved jelly-roll motif, forming a new structural family of enzymes.

Literature references that cite this PDB file's key reference

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PDB code: 3emr
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PDB codes: 2vcm 2ve1
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PDB code: 2r6s
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PDB code: 2jb4
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PDB codes: 1w3v 1w3x
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PDB codes: 1unb 1uo9 1uob 1uof 1uog
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PDB codes: 1w9y 1wa6
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PDB codes: 1j58 1l3j
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Reversal of DNA alkylation damage by two human dioxygenases.
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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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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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The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases.
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Mutational analysis of conserved glycines 42 and 256 in Cephalosporium acremonium isopenicillin N synthase.
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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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PDB code: 1ndo
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Primary structure, tissue distribution, and chromosomal localization of a novel isoform of lysyl hydroxylase (lysyl hydroxylase 3)
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Mutational evidence for the role of serine-283 in Cephalosporium acremonium isopenicillin N synthase.
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Oxygen activating nonheme iron enzymes.
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Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding.
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PDB codes: 3pca 3pcj 3pck 3pcl 3pcm
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The biosynthesis of plant alkaloids and nitrogenous microbial metabolites.
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Manganese(II) active site mutants of 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Arthrobacter globiformis strain CM-2.
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The x-ray crystal structure of phosphomannose isomerase from Candida albicans at 1.7 angstrom resolution.
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PDB code: 1pmi
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DIOXYGENASES: Molecular Structure and Role in Plant Metabolism.
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Asp537 and Asp812 in bacteriophage T7 RNA polymerase as metal ion-binding sites studied by EPR, flow-dialysis, and transcription.
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Ferrous active site of isopenicillin N synthase: genetic and sequence analysis of the endogenous ligands.
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A single monomeric iron center in clavaminate synthase catalyzes three nonsuccessive oxidative transformations.
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