6IIY

Crystal structure of deacetylase triple mutant (Orf2*T) that involving in teicoplanin biosynthetic pathway


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Teicoplanin Reprogrammed with the N-Acyl-Glucosamine Pharmacophore at the Penultimate Residue of Aglycone Acquires Broad-Spectrum Antimicrobial Activities Effectively Killing Gram-Positive and -Negative Pathogens.

Huang, C.M.Lyu, S.Y.Lin, K.H.Chen, C.L.Chen, M.H.Shih, H.W.Hsu, N.S.Lo, I.W.Wang, Y.L.Li, Y.S.Wu, C.J.Li, T.L.

(2019) ACS Infect Dis 5: 430-442

  • DOI: https://doi.org/10.1021/acsinfecdis.8b00317
  • Primary Citation of Related Structures:  
    6IIX, 6IIY

  • PubMed Abstract: 

    Lipoglycopeptide antibiotics, for example, teicoplanin (Tei) and A40926, are more potent than vancomycin against Gram-positive (Gram-(+)) drug-resistant pathogens, for example, methicillin-resistant Staphylococcus aureus (MRSA). To extend their therapeutic effectiveness on vancomycin-resistant S. aureus (VRSA), the biosynthetic pathway of the N-acyl glucosamine (Glc) pharmacophore at residue 4 (r4) of teicoplanin pseudoaglycone redirection to residue 6 (r6) was attempted. On the basis of crystal structures, two regioselective biocatalysts Orf2*T (a triple-mutation mutant S98A/V121A/F193Y) and Orf11*S (a single-mutation mutant W163A) were engineered, allowing them to act on GlcNAc at r6. New analogs thereby made show marked antimicrobial activity against MRSA and VRSA by 2-3 orders of magnitude better than teicoplanin and vancomycin. The lipid side chain of the Tei-analogs armed with a terminal mono- or diguanidino group extends the antimicrobial specificity from Gram-(+) to Gram-negative (Gram-(-)), comparable to that of kanamycin. In addition to low cytotoxicity and high safety, the Tei analogs exhibit new modes of action as a result of resensitization of VRSA and Acinetobacter baumannii. The redirection of the biosynthetic pathway for the N-acyl-Glc pharmacophore from r4 to r6 bodes well for large-scale production of selected r6,Tei congeners in an environmentally friendly synthetic biology approach.


  • Organizational Affiliation

    Genomics Research Center , Academia Sinica , 128 Academia Road , Section 2, Nankang, Taipei 11529 , Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
deacetylase293Actinoplanes teichomyceticusMutation(s): 3 
Gene Names: tcp14
UniProt
Find proteins for Q6ZZJ1 (Actinoplanes teichomyceticus)
Explore Q6ZZJ1 
Go to UniProtKB:  Q6ZZJ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6ZZJ1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.451α = 90
b = 66.671β = 92.59
c = 43.39γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Derived calculations
  • Version 1.2: 2020-10-21
    Changes: Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description