PDBsum entry 2ivi

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Oxidoreductase PDB id
Protein chain
329 a.a. *
SO4 ×2
Waters ×383
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: Isopenicillin n synthase from aspergillus nidulans (anaerobic ac-methyl-cyclopropylglycine fe complex)
Structure: Isopenicillin n synthetase. Chain: b. Synonym: ipns, isopenicillin n synthase. Engineered: yes
Source: Emericella nidulans. Organism_taxid: 162425. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.30Å     R-factor:   0.132     R-free:   0.157
Authors: J.M.Elkins,A.R.Howard-Jones,I.J.Clifton,P.L.Roach, R.M.Adlington,J.E.Baldwin,P.J.Rutledge
Key ref: A.R.Howard-Jones et al. (2007). Interactions of isopenicillin N synthase with cyclopropyl-containing substrate analogues reveal new mechanistic insight. Biochemistry, 46, 4755-4762. PubMed id: 17397141 DOI: 10.1021/bi062314q
13-Jun-06     Release date:   10-Apr-07    
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 = ACW)
matches with 96.00% similarity
+ 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: 10.1021/bi062314q Biochemistry 46:4755-4762 (2007)
PubMed id: 17397141  
Interactions of isopenicillin N synthase with cyclopropyl-containing substrate analogues reveal new mechanistic insight.
A.R.Howard-Jones, J.M.Elkins, I.J.Clifton, P.L.Roach, R.M.Adlington, J.E.Baldwin, P.J.Rutledge.
Isopenicillin N synthase (IPNS), a non-heme iron oxidase central to penicillin and cephalosporin biosynthesis, catalyzes an energetically demanding chemical transformation to produce isopenicillin N from the tripeptide delta-(l-alpha-aminoadipoyl)-l-cysteinyl-d-valine (ACV). We describe the synthesis of two cyclopropyl-containing tripeptide analogues, delta-(l-alpha-aminoadipoyl)-l-cysteinyl-beta-methyl-d-cyclopropylglycine and delta-(l-alpha-aminoadipoyl)-l-cysteinyl-d-cyclopropylglycine, designed as probes for the mechanism of IPNS. We have solved the X-ray crystal structures of these substrates in complex with IPNS and propose a revised mechanism for the IPNS-mediated turnover of these compounds. Relative to the previously determined IPNS-Fe(II)-ACV structure, key differences exist in substrate orientation and water occupancy, which allow for an explanation of the differences in reactivity of these substrates.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20108010 C.H.Küchenthal, J.Migenda, M.Polednia, and W.Maison (2010).
An improved protocol for the preparation of (S)-vinylglycine from (S)-methionine.
  Amino Acids, 39, 443-448.  
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 code: 2vcm
19007887 J.D.Lipscomb (2008).
Mechanism of extradiol aromatic ring-cleaving dioxygenases.
  Curr Opin Struct Biol, 18, 644-649.  
18366686 L.Gidijala, R.A.Bovenberg, P.Klaassen, I.J.van der Klei, M.Veenhuis, and J.A.Kiel (2008).
Production of functionally active Penicillium chrysogenum isopenicillin N synthase in the yeast Hansenula polymorpha.
  BMC Biotechnol, 8, 29.  
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
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 code is shown on the right.