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PDBsum entry 1ips

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protein metals Protein-protein interface(s) links
Antibiotic biosynthesis PDB id
1ips
Jmol
Contents
Protein chains
328 a.a. *
Metals
_MN ×4
Waters ×194
* Residue conservation analysis
PDB id:
1ips
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)
Resolution:
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
Date:
21-Mar-97     Release date:   25-Mar-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Enzyme reactions 
   Enzyme class: E.C.1.21.3.1  - Isopenicillin-N synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Penicillin N and Deacetoxycephalosporin C Biosynthesis
      Reaction: N-((5S)-5-amino-5-carboxypentanoyl)-L-cysteinyl-D-valine + O2 = isopenicillin N + 2 H2O
N-((5S)-5-amino-5-carboxypentanoyl)-L-cysteinyl-D-valine
+ 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.
 
  ABSTRACT  
 
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

  PubMed id Reference
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In vivo self-hydroxylation of an iron-substituted manganese-dependent extradiol cleaving catechol dioxygenase.
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Regio- and stereodivergent antibiotic oxidative carbocyclizations catalysed by Rieske oxygenase-like enzymes.
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21209891 F.Dahmani-Mardas, C.Troadec, A.Boualem, S.Lévêque, A.A.Alsadon, A.A.Aldoss, C.Dogimont, and A.Bendahmane (2010).
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Crystal structure of Tpa1 from Saccharomyces cerevisiae, a component of the messenger ribonucleoprotein complex.
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PDB codes: 3kt1 3kt4 3kt7
20498719 K.Reuter, M.Pittelkow, J.Bursy, A.Heine, T.Craan, and E.Bremer (2010).
Synthesis of 5-hydroxyectoine from ectoine: crystal structure of the non-heme iron(II) and 2-oxoglutarate-dependent dioxygenase EctD.
  PLoS One, 5, e10647.
PDB code: 3emr
  19411852 L.M.Iyer, M.Tahiliani, A.Rao, and L.Aravind (2009).
Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids.
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18998159 R.Stracke, R.C.De Vos, L.Bartelniewoehner, H.Ishihara, M.Sagasser, S.Martens, and B.Weisshaar (2009).
Metabolomic and genetic analyses of flavonol synthesis in Arabidopsis thaliana support the in vivo involvement of leucoanthocyanidin dioxygenase.
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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
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.
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18391407 B.Lohkamp, and D.Dobritzsch (2008).
A mixture of fortunes: the curious determination of the structure of Escherichia coli BL21 Gab protein.
  Acta Crystallogr D Biol Crystallogr, 64, 407-415.
PDB code: 2r6s
18063574 E.Flashman, E.A.Bagg, R.Chowdhury, J.Mecinović, C.Loenarz, M.A.McDonough, K.S.Hewitson, and C.J.Schofield (2008).
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Production of functionally active Penicillium chrysogenum isopenicillin N synthase in the yeast Hansenula polymorpha.
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18238897 L.M.Mirica, and J.P.Klinman (2008).
The nature of O2 activation by the ethylene-forming enzyme 1-aminocyclopropane-1-carboxylic acid oxidase.
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Hydroquinone dioxygenase from pseudomonas fluorescens ACB: a novel member of the family of nonheme-iron(II)-dependent dioxygenases.
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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
17342411 A.Siddiq, L.R.Aminova, and R.R.Ratan (2007).
Hypoxia inducible factor prolyl 4-hydroxylase enzymes: center stage in the battle against hypoxia, metabolic compromise and oxidative stress.
  Neurochem Res, 32, 931-946.  
17506560 C.D.Brown, M.L.Neidig, M.B.Neibergall, J.D.Lipscomb, and E.I.Solomon (2007).
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.
  J Am Chem Soc, 129, 7427-7438.  
17325776 N.M.Carvalho, O.A.Antunes, and A.Horn (2007).
Electrochemical behaviour of mononuclear Fe(III) complexes as models for oxygenases: reactivity of Fe(II) species electrochemically formed in situ toward dioxygen.
  Dalton Trans, (), 1023-1027.  
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
16779664 G.Shen, Y.Pang, W.Wu, Z.Deng, L.Zhao, Y.Cao, X.Sun, and K.Tang (2006).
Cloning and characterization of a flavanone 3-hydroxylase gene from Ginkgo biloba.
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16705404 J.W.Hudgins, S.G.Ralph, V.R.Franceschi, and J.Bohlmann (2006).
Ethylene in induced conifer defense: cDNA cloning, protein expression, and cellular and subcellular localization of 1-aminocyclopropane-1-carboxylate oxidase in resin duct and phenolic parenchyma cells.
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16538615 P.J.Lyons, N.R.Mattatall, and H.S.Ro (2006).
Modeling and functional analysis of AEBP1, a transcriptional repressor.
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16895917 S.S.Yeong, Y.Zhu, D.Smith, C.Verma, W.G.Lim, B.J.Tan, Q.T.Li, N.S.Cheung, M.Cai, Y.Z.Zhu, S.F.Zhou, S.L.Tan, and W.Duan (2006).
The last 10 amino acid residues beyond the hydrophobic motif are critical for the catalytic competence and function of protein kinase Calpha.
  J Biol Chem, 281, 30768-30781.  
15725659 A.Nakayama, M.Nakajima, and I.Yamaguchi (2005).
Distribution of gibberellins and expressional analysis of GA 20-oxidase genes of morning glory during fruit maturation.
  Biosci Biotechnol Biochem, 69, 334-342.  
16332884 C.L.Wei, Y.B.Yang, C.H.Deng, W.C.Liu, J.S.Hsu, Y.C.Lin, S.H.Liaw, and Y.C.Tsai (2005).
Directed evolution of Streptomyces clavuligerus deacetoxycephalosporin C synthase for enhancement of penicillin G expansion.
  Appl Environ Microbiol, 71, 8873-8880.  
15739104 K.D.Koehntop, J.P.Emerson, and L.Que (2005).
The 2-His-1-carboxylate facial triad: a versatile platform for dioxygen activation by mononuclear non-heme iron(II) enzymes.
  J Biol Inorg Chem, 10, 87-93.  
16317455 M.L.Neidig, and E.I.Solomon (2005).
Structure-function correlations in oxygen activating non-heme iron enzymes.
  Chem Commun (Camb), (), 5843-5863.  
16113715 N.J.Kershaw, M.E.Caines, M.C.Sleeman, and C.J.Schofield (2005).
The enzymology of clavam and carbapenem biosynthesis.
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15032824 A.P.Calvo, C.Nicolás, G.Nicolás, and D.Rodríguez (2004).
Evidence of a cross-talk regulation of a GA 20-oxidase (FsGA20ox1) by gibberellins and ethylene during the breaking of dormancy in Fagus sylvatica seeds.
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15725058 B.S.Winkel (2004).
Metabolic channeling in plants.
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15122348 C.J.Schofield, and P.J.Ratcliffe (2004).
Oxygen sensing by HIF hydroxylases.
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15134335 E.Metzen, and P.J.Ratcliffe (2004).
HIF hydroxylation and cellular oxygen sensing.
  Biol Chem, 385, 223-230.  
15466573 J.S.Hsu, Y.B.Yang, C.H.Deng, C.L.Wei, S.H.Liaw, and Y.C.Tsai (2004).
Family shuffling of expandase genes to enhance substrate specificity for penicillin G.
  Appl Environ Microbiol, 70, 6257-6263.  
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
15086827 M.Del Carmen Rodríguez-Gacio, C.Nicolás, and A.J.Matilla (2004).
The final step of the ethylene biosynthesis pathway in turnip tops (Brassica rapa): molecular characterization of the 1-aminocyclopropane-1-carboxylate oxidase BrACO1 throughout zygotic embryogenesis and germination of heterogeneous seeds.
  Physiol Plant, 121, 132-140.  
15489165 Z.Zhang, J.S.Ren, I.J.Clifton, and C.J.Schofield (2004).
Crystal structure and mechanistic implications of 1-aminocyclopropane-1-carboxylic acid oxidase--the ethylene-forming enzyme.
  Chem Biol, 11, 1383-1394.
PDB codes: 1w9y 1wa6
12925778 E.Metzen, J.Zhou, W.Jelkmann, J.Fandrey, and B.Brüne (2003).
Nitric oxide impairs normoxic degradation of HIF-1alpha by inhibition of prolyl hydroxylases.
  Mol Biol Cell, 14, 3470-3481.  
14667252 M.A.Kurowski, A.S.Bhagwat, G.Papaj, and J.M.Bujnicki (2003).
Phylogenomic identification of five new human homologs of the DNA repair enzyme AlkB.
  BMC Genomics, 4, 48.  
12642663 M.J.Ryle, K.D.Koehntop, A.Liu, L.Que, and R.P.Hausinger (2003).
Interconversion of two oxidized forms of taurine/alpha-ketoglutarate dioxygenase, a non-heme iron hydroxylase: evidence for bicarbonate binding.
  Proc Natl Acad Sci U S A, 100, 3790-3795.  
12517444 T.J.Begley, and L.D.Samson (2003).
AlkB mystery solved: oxidative demethylation of N1-methyladenine and N3-methylcytosine adducts by a direct reversal mechanism.
  Trends Biochem Sci, 28, 2-5.  
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.  
12080085 D.Lando, D.J.Peet, J.J.Gorman, D.A.Whelan, M.L.Whitelaw, and R.K.Bruick (2002).
FIH-1 is an asparaginyl hydroxylase enzyme that regulates the transcriptional activity of hypoxia-inducible factor.
  Genes Dev, 16, 1466-1471.  
12180990 F.Wellmann, R.Lukacin, T.Moriguchi, L.Britsch, E.Schiltz, and U.Matern (2002).
Functional expression and mutational analysis of flavonol synthase from Citrus unshiu.
  Eur J Biochem, 269, 4134-4142.  
12146944 J.C.Dunning Hotopp, and R.P.Hausinger (2002).
Probing the 2,4-dichlorophenoxyacetate/alpha-ketoglutarate dioxygenase substrate-binding site by site-directed mutagenesis and mechanism-based inactivation.
  Biochemistry, 41, 9787-9794.  
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.
  Eur J Biochem, 268, 6625-6636.
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.
  Annu Rev Biochem, 70, 209-246.  
11223521 J.J.Turnbull, A.G.Prescott, C.J.Schofield, and R.C.Wilmouth (2001).
Purification, crystallization and preliminary X-ray diffraction of anthocyanidin synthase from Arabidopsis thaliana.
  Acta Crystallogr D Biol Crystallogr, 57, 425-427.  
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
  11276424 L.Aravind, and E.V.Koonin (2001).
The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases.
  Genome Biol, 2, RESEARCH0007.  
11718551 P.Loke, and T.S.Sim (2001).
Mutational analysis of conserved glycines 42 and 256 in Cephalosporium acremonium isopenicillin N synthase.
  Can J Microbiol, 47, 961-964.  
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.
  J Biol Chem, 275, 12400-12409.  
11142372 D.Drygin, and R.A.Zimmermann (2000).
Magnesium ions mediate contacts between phosphoryl oxygens at positions 2122 and 2176 of the 23S rRNA and ribosomal protein L1.
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10913275 N.Khaleeli, R.W.Busby, and C.A.Townsend (2000).
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.
  Biochemistry, 39, 8666-8673.  
10978157 N.M.Brunhuber, J.L.Mort, R.E.Christoffersen, and N.O.Reich (2000).
Steady-state kinetic mechanism of recombinant avocado ACC oxidase: initial velocity and inhibitor studies.
  Biochemistry, 39, 10730-10738.  
10651823 R.Lukacin, I.Gröning, U.Pieper, and U.Matern (2000).
Site-directed mutagenesis of the active site serine290 in flavanone 3beta-hydroxylase from Petunia hybrida.
  Eur J Biochem, 267, 853-860.  
10607676 C.J.Schofield, and Z.Zhang (1999).
Structural and mechanistic studies on 2-oxoglutarate-dependent oxygenases and related enzymes.
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10428773 M.Eriksson, J.Myllyharju, H.Tu, M.Hellman, and K.I.Kivirikko (1999).
Evidence for 4-hydroxyproline in viral proteins. Characterization of a viral prolyl 4-hydroxylase and its peptide substrates.
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  10049860 M.Watanabe, N.Sumida, S.Murakami, H.Anzai, C.J.Thompson, Y.Tateno, and T.Murakami (1999).
A phosphonate-induced gene which promotes Penicillium-mediated bioconversion of cis-propenylphosphonic acid to fosfomycin.
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10037780 P.Annunen, P.Koivunen, and K.I.Kivirikko (1999).
Cloning of the alpha subunit of prolyl 4-hydroxylase from Drosophila and expression and characterization of the corresponding enzyme tetramer with some unique properties.
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10227172 P.Loke, and T.S.Sim (1999).
Glutamine-230 influences enzyme solubility but not catalysis in Streptomyces clavuligerus isopenicillin N synthase.
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10518746 P.Loke, and T.Sim (1999).
Site-directed mutagenesis of arginine-89 supports the role of its guanidino side-chain in substrate binding by Cephalosporium acremonium isopenicillin N synthase.
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  10473412 T.Shibasaki, H.Mori, S.Chiba, and A.Ozaki (1999).
Microbial proline 4-hydroxylase screening and gene cloning.
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  9729600 A.A.Brakhage (1998).
Molecular regulation of beta-lactam biosynthesis in filamentous fungi.
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9634695 B.Kauppi, K.Lee, E.Carredano, R.E.Parales, D.T.Gibson, H.Eklund, and S.Ramaswamy (1998).
Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase.
  Structure, 6, 571-586.
PDB code: 1ndo
9545433 C.J.Rowe, C.P.Shorrock, T.D.Claridge, and J.D.Sutherland (1998).
Analysis of the conversion of delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-alpha-aminobutyrate by active-site mutants of Aspergillus nidulans isopenicillin N synthase.
  Chem Biol, 5, 229-239.  
9582318 M.Valtavaara, C.Szpirer, J.Szpirer, and R.Myllylä (1998).
Primary structure, tissue distribution, and chromosomal localization of a novel isoform of lysyl hydroxylase (lysyl hydroxylase 3)
  J Biol Chem, 273, 12881-12886.  
9841222 P.Loke, and T.S.Sim (1998).
Mutational evidence for the role of serine-283 in Cephalosporium acremonium isopenicillin N synthase.
  FEMS Microbiol Lett, 165, 353-356.  
9667935 S.J.Lange, and L.Que (1998).
Oxygen activating nonheme iron enzymes.
  Curr Opin Chem Biol, 2, 159-172.  
9254600 A.M.Orville, J.D.Lipscomb, and D.H.Ohlendorf (1997).
Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding.
  Biochemistry, 36, 10052-10066.
PDB codes: 3pca 3pcj 3pck 3pcl 3pcm
9375250 C.A.Townsend (1997).
Structural studies of natural product biosynthetic proteins.
  Chem Biol, 4, 721-730.  
9434907 C.J.Schofield, J.E.Baldwin, M.F.Byford, I.Clifton, J.Hajdu, C.Hensgens, and P.Roach (1997).
Proteins of the penicillin biosynthesis pathway.
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9238076 D.N.Martin, W.M.Proebsting, and P.Hedden (1997).
Mendel's dwarfing gene: cDNAs from the Le alleles and function of the expressed proteins.
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Characterization of alpha-ketoglutarate-dependent taurine dioxygenase from Escherichia coli.
  J Biol Chem, 272, 23031-23036.  
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The 2-His-1-carboxylate facial triad--an emerging structural motif in mononuclear non-heme iron(II) enzymes.
  Eur J Biochem, 250, 625-629.  
  9294421 H.Mori, T.Shibasaki, K.Yano, and A.Ozaki (1997).
Purification and cloning of a proline 3-hydroxylase, a novel enzyme which hydroxylates free L-proline to cis-3-hydroxy-L-proline.
  J Bacteriol, 179, 5677-5683.  
9135134 J.Myllyharju, and K.I.Kivirikko (1997).
Characterization of the iron- and 2-oxoglutarate-binding sites of human prolyl 4-hydroxylase.
  EMBO J, 16, 1173-1180.  
9281835 K.H.Baggaley, A.G.Brown, and C.J.Schofield (1997).
Chemistry and biosynthesis of clavulanic acid and other clavams.
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  9352915 K.Nickel, M.J.Suter, and H.P.Kohler (1997).
Involvement of two alpha-ketoglutarate-dependent dioxygenases in enantioselective degradation of (R)- and (S)-mecoprop by Sphingomonas herbicidovorans MH.
  J Bacteriol, 179, 6674-6679.  
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Functional analysis of a conserved aspartate D218 in Cephalosporium acremonium isopenicillin N synthase.
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PDB code: 1pmi
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