5X5M | pdb_00005x5m

Crystal structure of a hydrolase encoded by lin2189 from Listeria innocua


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free: 
    0.195 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.1 of the entry. See complete history


Literature

GyrI-like proteins catalyze cyclopropanoid hydrolysis to confer cellular protection

Yuan, H.Zhang, J.Cai, Y.Wu, S.Yang, K.Chan, H.C.S.Huang, W.Jin, W.B.Li, Y.Yin, Y.Igarashi, Y.Yuan, S.Zhou, J.Tang, G.L.

(2017) Nat Commun 8: 1485-1485

  • DOI: https://doi.org/10.1038/s41467-017-01508-1
  • Primary Citation of Related Structures:  
    5X5M

  • PubMed Abstract: 

    GyrI-like proteins are widely distributed in prokaryotes and eukaryotes, and recognized as small-molecule binding proteins. Here, we identify a subfamily of these proteins as cyclopropanoid cyclopropyl hydrolases (CCHs) that can catalyze the hydrolysis of the potent DNA-alkylating agents yatakemycin (YTM) and CC-1065. Co-crystallography and molecular dynamics simulation analyses reveal that these CCHs share a conserved aromatic cage for the hydrolytic activity. Subsequent cytotoxic assays confirm that CCHs are able to protect cells against YTM. Therefore, our findings suggest that the evolutionarily conserved GyrI-like proteins confer cellular protection against diverse xenobiotics via not only binding, but also catalysis.


  • Organizational Affiliation

    State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lin2189 protein
A, B
216Listeria innocua Clip11262Mutation(s): 2 
Gene Names: lin2189
UniProt
Find proteins for Q929T5 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262))
Explore Q929T5 
Go to UniProtKB:  Q929T5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ929T5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.21 Å
  • R-Value Free:  0.195 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.63α = 90
b = 49.295β = 124.98
c = 80.361γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data processing
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 7YUClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2017-12-06 
  • Deposition Author(s): Zhang, J.

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description