7Y4H

AcvX from Actinomadura viridis that exhibits deglycosylation activity on lobophorins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A Widespread Glycosidase Confers Lobophorin Resistance and Host-Dependent Structural Diversity.

Tan, B.Zhang, L.Zhang, Q.Chen, S.Xiong, W.Zhu, Y.Zhang, C.

(2023) Angew Chem Int Ed Engl 62: e202302043-e202302043

  • DOI: https://doi.org/10.1002/anie.202302043
  • Primary Citation of Related Structures:  
    7Y4H

  • PubMed Abstract: 

    Identifying new environmental resistance determinants is significant to combat rising antibiotic resistance. Herein we report the unexpected correlation of a lobophorin (LOB) resistance-related glycosidase KijX with the host-dependent chemical diversity of LOBs, by a process of glycosylation, deglycosylation and reglycosylation. KijX homologues are widespread among bacteria, archaea and fungi, and encode the same glycohydrolytic activity on LOBs. The crystal structure of AcvX (a KijX homologue) shows a similar fold to that of the glycoside hydrolase family 113 and a special negatively charged groove to accommodate and deglycosylate LOBs. Antagonistic assays indicate kijX as a defense weapon of actinomycetes to combat LOB producers in environment, reflecting an elegant coevolution relationship. Our study provides insight into the KijX-related glycosidases as preexisting resistance determinants and represents an example of resistance genes accidentally integrated into natural product assembly.


  • Organizational Affiliation

    Key Laboratory of Tropical Marine Bioresources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Science, Guangzhou, 510301, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AcvX338Actinomadura viridisMutation(s): 0 
UniProt
Find proteins for A0A931GJG6 (Actinomadura viridis)
Explore A0A931GJG6 
Go to UniProtKB:  A0A931GJG6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A931GJG6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.588α = 90
b = 66.605β = 90
c = 153.585γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32100045
National Natural Science Foundation of China (NSFC)China31820103003
National Natural Science Foundation of China (NSFC)China22193072
National Natural Science Foundation of China (NSFC)China22177118

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-07-12
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Refinement description