SDR protein NapW-NADP

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Reductive inactivation of the hemiaminal pharmacophore for resistance against tetrahydroisoquinoline antibiotics.

Wen, W.H.Zhang, Y.Zhang, Y.Y.Yu, Q.Jiang, C.C.Tang, M.C.Pu, J.Y.Wu, L.Zhao, Y.L.Shi, T.Zhou, J.Tang, G.L.

(2021) Nat Commun 12: 7085-7085

  • DOI: https://doi.org/10.1038/s41467-021-27404-3
  • Primary Citation of Related Structures:  
    7BSX, 7BTM

  • PubMed Abstract: 

    Antibiotic resistance is becoming one of the major crises, among which hydrolysis reaction is widely employed by bacteria to destroy the reactive pharmacophore. Correspondingly, antibiotic producer has canonically co-evolved this approach with the biosynthetic capability for self-resistance. Here we discover a self-defense strategy featuring with reductive inactivation of hemiaminal pharmacophore by short-chain dehydrogenases/reductases (SDRs) NapW and homW, which are integrated with the naphthyridinomycin biosynthetic pathway. We determine the crystal structure of NapW·NADPH complex and propose a catalytic mechanism by molecular dynamics simulation analysis. Additionally, a similar detoxification strategy is identified in the biosynthesis of saframycin A, another member of tetrahydroisoquinoline (THIQ) antibiotics. Remarkably, similar SDRs are widely spread in bacteria and able to inactive other THIQ members including the clinical anticancer drug, ET-743. These findings not only fill in the missing intracellular events of temporal-spatial shielding mode for cryptic self-resistance during THIQs biosynthesis, but also exhibit a sophisticated damage-control in secondary metabolism and general immunity toward this family of antibiotics.

  • Organizational Affiliation

    State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Short chain dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H
331Streptomyces lusitanusMutation(s): 0 
Find proteins for S4TKM8 (Streptomyces lusitanus)
Explore S4TKM8 
Go to UniProtKB:  S4TKM8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS4TKM8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.42α = 90
b = 116.04β = 90.04
c = 134.76γ = 90
Software Package:
Software NamePurpose
xia2data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31930002

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-06
    Type: Initial release
  • Version 1.1: 2021-12-22
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description