1IPS | pdb_00001ips

ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (MANGANESE COMPLEX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.265 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.220 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of isopenicillin N synthase is the first from a new structural family of enzymes.

Roach, P.L.Clifton, I.J.Fulop, V.Harlos, K.Barton, G.J.Hajdu, J.Andersson, I.Schofield, C.J.Baldwin, J.E.

(1995) Nature 375: 700-704

  • DOI: https://doi.org/10.1038/375700a0
  • Primary Citation Related Structures: 
    1IPS

  • PubMed 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.


  • Organizational Affiliation
    • Dyson Perrins Laboratory, University of Oxford, UK.

Macromolecule Content 

  • Total Structure Weight: 75.35 kDa 
  • Atom Count: 5,476 
  • Modeled Residue Count: 656 
  • Deposited Residue Count: 662 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ISOPENICILLIN N SYNTHASE
A, B
331Aspergillus nidulansMutation(s): 0 
Gene Names: PCB C
EC: 1.21.3.1
UniProt
Find proteins for P05326 (Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139))
Explore P05326 
Go to UniProtKB:  P05326
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05326
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.265 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.220 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.2α = 90
b = 127β = 90
c = 139.6γ = 90
Software Package:
Software NamePurpose
DMmodel building
MLPHAREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-03-25
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations