PDBsum entry 1ips

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Antibiotic biosynthesis PDB id
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 DOI: 10.1038/375700a0
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     biosynthetic process   5 terms 
  Biochemical function     oxidoreductase activity     7 terms  


    Added reference    
DOI no: 10.1038/375700a0 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 codes: 3kt1 3kt4 3kt7
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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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VTVH-MCD and DFT studies of thiolate bonding to [FeNO]7/[FeO2]8 complexes of isopenicillin N synthase: substrate determination of oxidase versus oxygenase activity in nonheme Fe enzymes.
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PDB codes: 1w3v 1w3x
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Cloning and characterization of a flavanone 3-hydroxylase gene from Ginkgo biloba.
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PDB codes: 1unb 1uo9 1uob 1uof 1uog
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PDB codes: 1w9y 1wa6
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FIH-1 is an asparaginyl hydroxylase enzyme that regulates the transcriptional activity of hypoxia-inducible factor.
  Genes Dev, 16, 1466-1471.  
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Probing the 2,4-dichlorophenoxyacetate/alpha-ketoglutarate dioxygenase substrate-binding site by site-directed mutagenesis and mechanism-based inactivation.
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12056897 R.Anand, P.C.Dorrestein, C.Kinsland, T.P.Begley, and S.E.Ealick (2002).
Structure of oxalate decarboxylase from Bacillus subtilis at 1.75 A resolution.
  Biochemistry, 41, 7659-7669.
PDB codes: 1j58 1l3j
12486230 T.Duncan, S.C.Trewick, P.Koivisto, P.A.Bates, T.Lindahl, and B.Sedgwick (2002).
Reversal of DNA alkylation damage by two human dioxygenases.
  Proc Natl Acad Sci U S A, 99, 16660-16665.  
11717489 A.C.Terwisscha van Scheltinga, K.Valegård, S.Ramaswamy, J.Hajdu, and I.Andersson (2001).
Multiple isomorphous replacement on merohedral twins: structure determination of deacetoxycephalosporin C synthase.
  Acta Crystallogr D Biol Crystallogr, 57, 1776-1785.  
11737217 I.J.Clifton, L.C.Hsueh, J.E.Baldwin, K.Harlos, and C.J.Schofield (2001).
Structure of proline 3-hydroxylase. Evolution of the family of 2-oxoglutarate dependent oxygenases.
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PDB codes: 1e5r 1e5s
11395407 J.A.Gerlt, and P.C.Babbitt (2001).
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
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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.
  Chem Biol, 8, 1231-1237.
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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11718551 P.Loke, and T.S.Sim (2001).
Mutational analysis of conserved glycines 42 and 256 in Cephalosporium acremonium isopenicillin N synthase.
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10777523 D.A.Hogan, S.R.Smith, E.A.Saari, J.McCracken, and R.P.Hausinger (2000).
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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11142372 D.Drygin, and R.A.Zimmermann (2000).
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Site-directed mutagenesis and biochemical analysis of the endogenous ligands in the ferrous active site of clavaminate synthase. The His-3 variant of the 2-His-1-carboxylate model.
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Structural and mechanistic studies on 2-oxoglutarate-dependent oxygenases and related enzymes.
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Evidence for 4-hydroxyproline in viral proteins. Characterization of a viral prolyl 4-hydroxylase and its peptide substrates.
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Microbial proline 4-hydroxylase screening and gene cloning.
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Molecular regulation of beta-lactam biosynthesis in filamentous fungi.
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Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase.
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PDB code: 1ndo
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Analysis of the conversion of delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-alpha-aminobutyrate by active-site mutants of Aspergillus nidulans isopenicillin N synthase.
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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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Structural studies of natural product biosynthetic proteins.
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Proteins of the penicillin biosynthesis pathway.
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Characterization of alpha-ketoglutarate-dependent taurine dioxygenase from Escherichia coli.
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Involvement of two alpha-ketoglutarate-dependent dioxygenases in enantioselective degradation of (R)- and (S)-mecoprop by Sphingomonas herbicidovorans MH.
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Functional analysis of a conserved aspartate D218 in Cephalosporium acremonium isopenicillin N synthase.
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The biosynthesis of plant alkaloids and nitrogenous microbial metabolites.
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Identification of strictly conserved histidine and arginine residues as part of the active site in Petunia hybrida flavanone 3beta-hydroxylase.
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Cloning gibberellin dioxygenase genes from pumpkin endosperm by heterologous expression of enzyme activities in Escherichia coli.
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Manganese(II) active site mutants of 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Arthrobacter globiformis strain CM-2.
  Biochemistry, 36, 2147-2153.  
8612079 A.Cleasby, A.Wonacott, T.Skarzynski, R.E.Hubbard, G.J.Davies, A.E.Proudfoot, A.R.Bernard, M.A.Payton, and T.N.Wells (1996).
The x-ray crystal structure of phosphomannose isomerase from Candida albicans at 1.7 angstrom resolution.
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PDB code: 1pmi
15012289 A.G.Prescott, and P.John (1996).
DIOXYGENASES: Molecular Structure and Role in Plant Metabolism.
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8555168 A.Y.Woody, S.S.Eaton, P.A.Osumi-Davis, and R.W.Woody (1996).
Asp537 and Asp812 in bacteriophage T7 RNA polymerase as metal ion-binding sites studied by EPR, flow-dialysis, and transcription.
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Phylogenetic analysis of the isopenicillin-N-synthetase horizontal gene transfer.
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Functional analysis of conserved histidine residues in Cephalosporium acremonium isopenicillin N synthase by site-directed mutagenesis.
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Detection of Novel Proline 3-Hydroxylase Activities in Streptomyces and Bacillus spp. by Regio- and Stereospecific Hydroxylation of l-Proline.
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Ferrous active site of isopenicillin N synthase: genetic and sequence analysis of the endogenous ligands.
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Anaerobic crystallisation of an isopenicillin N synthase.Fe(II).substrate complex demonstrated by X-ray studies.
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A single monomeric iron center in clavaminate synthase catalyzes three nonsuccessive oxidative transformations.
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Heterologous expression and site-directed mutagenesis of the 1-aminocyclopropane-1-carboxylate oxidase from kiwi fruit.
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X-ray absorption spectroscopic studies of the FeZn derivative of uteroferrin.
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