6JYV | pdb_00006jyv

Structure of an isopenicillin N synthase from Pseudomonas aeruginosa PAO1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 
    0.208 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.165 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural characterization of an isopenicillin N synthase family oxygenase from Pseudomonas aeruginosa PAO1.

Zhang, H.Che, S.Wang, R.Liu, R.Zhang, Q.Bartlam, M.

(2019) Biochem Biophys Res Commun 514: 1031-1036

  • DOI: https://doi.org/10.1016/j.bbrc.2019.05.062
  • Primary Citation Related Structures: 
    6JYV

  • PubMed Abstract: 

    Isopenicillin N synthase (IPNS) is a nonheme-Fe 2+ -dependent enzyme that mediates a key step in penicillin biosynthesis. It catalyses the conversion of the tripeptide δ-(l-α-aminoadipoyl)-l-cysteine-d-valine (ACV) to isopenicillin N, which is a key precursor to β-lactam antibiotics. The pa4191 gene in Pseudomonas aeruginosa PAO1 has provisionally been annotated as a member of the IPNS family. In this work, we report the crystal structure of PA4191 from P. aeruginosa (PaIPNS hereafter). The 1.65 Å resolution PaIPNS structure forms a jelly roll fold and is confirmed to be a member of the IPNS family based on structural homology. A metal centre within the jelly roll consists of the strictly conserved His201, Asp203 and His257 residues. MicroScale Thermophoresis binding analysis confirms that PaIPNS is a metal-binding protein with a strong preference for iron, but that it does not bind the tripeptide ACV. Structural comparison of PaIPNS with a previously reported IPNS-ACV complex structure reveals a restricted binding pocket that is unable to accommodate ACV.


  • Organizational Affiliation
    • College of Life Sciences, Nankai University, Tianjin, 300071, China.

Macromolecule Content 

  • Total Structure Weight: 75.84 kDa 
  • Atom Count: 6,445 
  • Modeled Residue Count: 657 
  • Deposited Residue Count: 678 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable iron/ascorbate oxidoreductase
A, B
339Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: PA4191
EC: 1.14.20.7 (UniProt), 1.13.12.19 (UniProt)
UniProt
Find proteins for Q9HWJ0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HWJ0 
Go to UniProtKB:  Q9HWJ0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HWJ0
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free:  0.208 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.165 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.51α = 90
b = 115.69β = 90.9
c = 68.83γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31570128

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.2: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description