7XX4 | pdb_00007xx4

designed glycosyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 
    0.239 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.216 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Design of a chimeric glycosyltransferase OleD for the site-specific O-monoglycosylation of 3-hydroxypyridine in nosiheptide.

Zhao, L.Xu, Y.Chen, M.Wu, L.Li, M.Lu, Y.Lu, M.Chen, Y.Wu, X.

(2023) Microb Biotechnol 16: 1971-1984

  • DOI: https://doi.org/10.1111/1751-7915.14332
  • Primary Citation Related Structures: 
    7XX4

  • PubMed Abstract: 

    To identify the potential role of the 3-hydroxyl group of the pyridine ring in nosiheptide (NOS) for its antibacterial activity against Gram-positive pathogens, enzymatic glycosylation was utilized to regio-selectively create a monoglycosyl NOS derivative, NOS-G. For this purpose, we selected OleD, a UDP glycosyltransferase from Streptomyces antibioticus that has a low productivity for NOS-G. Activity of the enzyme was increased by swapping domains derived from OleI, both single and in combination. Activity enhancement was best in mutant OleD-10 that contained four OleI domains. This chimer was engineered by site-directed mutagenesis (single and in combination) to increase its activity further, whereby variants were screened using a newly-established colorimetric assay. OleD-10 with I117F and T118G substitutions (FG) had an increased NOS-G productivity of 56%, approximately 70 times higher than that of wild-type OleD. The reason for improved activity of FG towards NOS was structurally attributed to a closer distance (<3 Å) between NOS/sugar donor and the catalytic amino acid H25. The engineered enzyme allowed sufficient activity to demonstrate that the produced NOS-G had enhanced stability and aqueous solubility compared to NOS. Using a murine MRSA infection model, it was established that NOS-G resulted in partial protection within 20 h of administration and delayed the death of infected mice. We conclude that 3-hydroxypyridine is a promising site for structural modification of NOS, which may pave the way for producing nosiheptide derivatives as a potential antibiotic for application in clinical treatment.


  • Organizational Affiliation
    • Laboratory of Chemical Biology, College of Life Sciences and Technology, China Pharmaceutical University, Nanjing, Jiangsu Province, PR China.

Macromolecule Content 

  • Total Structure Weight: 90.69 kDa 
  • Atom Count: 6,166 
  • Modeled Residue Count: 788 
  • Deposited Residue Count: 816 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Oleandomycin glycosyltransferase
A, B
408Streptomyces antibioticusMutation(s): 32 
Gene Names: oleD
UniProt
Find proteins for Q3HTL6 (Streptomyces antibioticus)
Explore Q3HTL6 
Go to UniProtKB:  Q3HTL6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3HTL6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free:  0.239 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.216 (DCC) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.716α = 90
b = 92.285β = 90
c = 191.438γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2023-06-14 
  • Deposition Author(s): Lu, M., Wu, X.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81973214

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-12-27
    Changes: Database references