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PDBsum entry 1bk0

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B-lactam antibiotic PDB id
1bk0
Jmol
Contents
Protein chain
329 a.a. *
Ligands
SO4
ACV
Metals
_FE
Waters ×323
* Residue conservation analysis
PDB id:
1bk0
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.
Resolution:
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
Date:
14-Jul-98     Release date:   13-Jan-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P05326  (IPNS_EMENI) -  Isopenicillin N synthase
Seq:
Struc:
331 a.a.
329 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
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     biosynthetic process   5 terms 
  Biochemical function     oxidoreductase activity     7 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.
 
  ABSTRACT  
 
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

  PubMed id Reference
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Engineering melon plants with improved fruit shelf life using the TILLING approach.
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PDB codes: 3hqr 3hqu
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Structural studies on the reaction of isopenicillin N synthase with a sterically demanding depsipeptide substrate analogue.
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PDB codes: 2vcm 2ve1
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Metal ions in biological catalysis: from enzyme databases to general principles.
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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).
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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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17235343 E.Flashman, and C.J.Schofield (2007).
The most versatile of all reactive intermediates?
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17374503 J.M.Bollinger, and C.Krebs (2007).
Enzymatic C-H activation by metal-superoxo intermediates.
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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
17045919 C.Schöneich, and V.S.Sharov (2006).
Mass spectrometry of protein modifications by reactive oxygen and nitrogen species.
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NO binding to naphthalene dioxygenase.
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PDB codes: 1uuv 1uuw
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The structure at 2.4 A resolution of the protein from gene locus At3g21360, a putative Fe(II)/2-oxoglutarate-dependent enzyme from Arabidopsis thaliana.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 469-472.
PDB code: 1y0z
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.
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Structural insight into antibiotic fosfomycin biosynthesis by a mononuclear iron enzyme.
  Nature, 437, 838-844.
PDB codes: 1zz6 1zz7 1zz8 1zz9 1zzb 1zzc
15654104 M.J.Spiering, C.D.Moon, H.H.Wilkinson, and C.L.Schardl (2005).
Gene clusters for insecticidal loline alkaloids in the grass-endophytic fungus Neotyphodium uncinatum.
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The enzymology of clavam and carbapenem biosynthesis.
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Anthocyanidin synthase in non-anthocyanin-producing Caryophyllales species.
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C-terminus mutations of Acremonium chrysogenum deacetoxy/deacetylcephalosporin C synthase with improved activity toward penicillin analogs.
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The cis-Pro touch-turn: a rare motif preferred at functional sites.
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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
12676714 C.L.Wei, Y.B.Yang, W.C.Wang, W.C.Liu, J.S.Hsu, and Y.C.Tsai (2003).
Engineering Streptomyces clavuligerus deacetoxycephalosporin C synthase for optimal ring expansion activity toward penicillin G.
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12482756 C.Lee, S.J.Kim, D.G.Jeong, S.M.Lee, and S.E.Ryu (2003).
Structure of human FIH-1 reveals a unique active site pocket and interaction sites for HIF-1 and von Hippel-Lindau.
  J Biol Chem, 278, 7558-7563.
PDB code: 1iz3
12591920 D.K.Kang, J.Jeong, S.K.Drake, N.B.Wehr, T.A.Rouault, and R.L.Levine (2003).
Iron regulatory protein 2 as iron sensor. Iron-dependent oxidative modification of cysteine.
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12603311 D.Lando, J.J.Gorman, M.L.Whitelaw, and D.J.Peet (2003).
Oxygen-dependent regulation of hypoxia-inducible factors by prolyl and asparaginyl hydroxylation.
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12598659 E.I.Solomon, A.Decker, and N.Lehnert (2003).
Non-heme iron enzymes: contrasts to heme catalysis.
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14529267 P.Liu, A.Liu, F.Yan, M.D.Wolfe, J.D.Lipscomb, and H.W.Liu (2003).
Biochemical and spectroscopic studies on (S)-2-hydroxypropylphosphonic acid epoxidase: a novel mononuclear non-heme iron enzyme.
  Biochemistry, 42, 11577-11586.  
12517755 R.W.Welford, I.Schlemminger, L.A.McNeill, K.S.Hewitson, and C.J.Schofield (2003).
The selectivity and inhibition of AlkB.
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12161433 A.K.White, and W.W.Metcalf (2002).
Isolation and biochemical characterization of hypophosphite/2-oxoglutarate dioxygenase. A novel phosphorus-oxidizing enzyme from Psuedomonas stutzeri WM88.
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11966408 A.Serretti (2002).
Lithium long-term treatment in mood disorders: clinical and genetic predictors.
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12432100 C.E.Dann, R.K.Bruick, and J.Deisenhofer (2002).
Structure of factor-inhibiting hypoxia-inducible factor 1: An asparaginyl hydroxylase involved in the hypoxic response pathway.
  Proc Natl Acad Sci U S A, 99, 15351-15356.
PDB codes: 1mze 1mzf
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.  
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.  
11939775 G.C.Ferreira, R.Franco, A.Mangravita, and G.N.George (2002).
Unraveling the substrate-metal binding site of ferrochelatase: an X-ray absorption spectroscopic study.
  Biochemistry, 41, 4809-4818.  
11910018 M.R.Chance, A.R.Bresnick, S.K.Burley, J.S.Jiang, C.D.Lima, A.Sali, S.C.Almo, J.B.Bonanno, J.A.Buglino, S.Boulton, H.Chen, N.Eswar, G.He, R.Huang, V.Ilyin, L.McMahan, U.Pieper, S.Ray, M.Vidal, and L.K.Wang (2002).
Structural genomics: a pipeline for providing structures for the biologist.
  Protein Sci, 11, 723-738.
PDB code: 1jr7
12077303 W.Spielmeyer, M.H.Ellis, and P.M.Chandler (2002).
Semidwarf (sd-1), "green revolution" rice, contains a defective gibberellin 20-oxidase gene.
  Proc Natl Acad Sci U S A, 99, 9043-9048.  
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
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.  
10985764 B.O.Bachmann, and C.A.Townsend (2000).
Kinetic mechanism of the beta-lactam synthetase of Streptomyces clavuligerus.
  Biochemistry, 39, 11187-11193.  
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.  
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.  
11091371 W.A.Schenk (2000).
Isopenicillin N Synthase: An Enzyme at Work.
  Angew Chem Int Ed Engl, 39, 3409-3411.  
10393920 A.M.Rocklin, D.L.Tierney, V.Kofman, N.M.Brunhuber, B.M.Hoffman, R.E.Christoffersen, N.O.Reich, J.D.Lipscomb, and L.Que (1999).
Role of the nonheme Fe(II) center in the biosynthesis of the plant hormone ethylene.
  Proc Natl Acad Sci U S A, 96, 7905-7909.  
10607676 C.J.Schofield, and Z.Zhang (1999).
Structural and mechanistic studies on 2-oxoglutarate-dependent oxygenases and related enzymes.
  Curr Opin Struct Biol, 9, 722-731.  
10600135 E.L.Hegg, A.K.Whiting, R.E.Saari, J.McCracken, R.P.Hausinger, and L.Que (1999).
Herbicide-degrading alpha-keto acid-dependent enzyme TfdA: metal coordination environment and mechanistic insights.
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10563813 M.J.Ryle, R.Padmakumar, and R.P.Hausinger (1999).
Stopped-flow kinetic analysis of Escherichia coli taurine/alpha-ketoglutarate dioxygenase: interactions with alpha-ketoglutarate, taurine, and oxygen.
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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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Molecular regulation of beta-lactam biosynthesis in filamentous fungi.
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9804844 A.M.Reeve, S.D.Breazeale, and C.A.Townsend (1998).
Purification, characterization, and cloning of an S-adenosylmethionine-dependent 3-amino-3-carboxypropyltransferase in nocardicin biosynthesis.
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Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase.
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PDB code: 1ndo
9689037 B.O.Bachmann, R.Li, and C.A.Townsend (1998).
beta-Lactam synthetase: a new biosynthetic enzyme.
  Proc Natl Acad Sci U S A, 95, 9082-9086.  
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.
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9748332 J.C.Milne, A.C.Eliot, N.L.Kelleher, and C.T.Walsh (1998).
ATP/GTP hydrolysis is required for oxazole and thiazole biosynthesis in the peptide antibiotic microcin B17.
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9841222 P.Loke, and T.S.Sim (1998).
Mutational evidence for the role of serine-283 in Cephalosporium acremonium isopenicillin N synthase.
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The axial tyrosinate Fe3+ ligand in protocatechuate 3,4-dioxygenase influences substrate binding and product release: evidence for new reaction cycle intermediates.
  Biochemistry, 37, 2131-2144.
PDB code: 3pcd
9667935 S.J.Lange, and L.Que (1998).
Oxygen activating nonheme iron enzymes.
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9375250 C.A.Townsend (1997).
Structural studies of natural product biosynthetic proteins.
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Proteins of the penicillin biosynthesis pathway.
  Curr Opin Struct Biol, 7, 857-864.  
9461283 E.L.Hegg, and L.Que (1997).
The 2-His-1-carboxylate facial triad--an emerging structural motif in mononuclear non-heme iron(II) enzymes.
  Eur J Biochem, 250, 625-629.  
9418249 P.Loke, J.Sim, and T.S.Sim (1997).
Functional analysis of a conserved aspartate D218 in Cephalosporium acremonium isopenicillin N synthase.
  FEMS Microbiol Lett, 157, 137-140.  
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.