7VYY

The crystal structure of Non-hydrolyzing UDPGlcNAc 2-epimerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.228 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

KasQ an Epimerase Primes the Biosynthesis of Aminoglycoside Antibiotic Kasugamycin and KasF/H Acetyltransferases Inactivate Its Activity.

Rattinam, R.Basha, R.S.Wang, Y.L.Wang, Z.C.Hsu, N.S.Lin, K.H.Zadeh, S.M.Adhikari, K.Lin, J.P.Li, T.L.

(2022) Biomedicines 10

  • DOI: https://doi.org/10.3390/biomedicines10020212
  • Primary Citation of Related Structures:  
    7VYY, 7VZ6, 7VZA

  • PubMed Abstract: 

    Kasugamycin (KSM), an aminoglycoside antibiotic, is composed of three chemical moieties: D- chiro -inositol, kasugamine and glycine imine. Despite being discovered more than 50 years ago, the biosynthetic pathway of KSM remains an unresolved puzzle. Here we report a structural and functional analysis for an epimerase, KasQ, that primes KSM biosynthesis rather than the previously proposed KasF/H, which instead acts as an acetyltransferase, inactivating KSM. Our biochemical and biophysical analysis determined that KasQ converts UDP-GlcNAc to UDP-ManNAc as the initial step in the biosynthetic pathway. The isotope-feeding study further confirmed that 13 C, 15 N-glucosamine/UDP-GlcNH 2 rather than glucose/UDP-Glc serves as the direct precursor for the formation of KSM. Both KasF and KasH were proposed, respectively, converting UDP-GlcNH 2 and KSM to UDP-GlcNAc and 2-N'-acetyl KSM. Experimentally, KasF is unable to do so; both KasF and KasH are instead KSM-modifying enzymes, while the latter is more specific and reactive than the former in terms of the extent of resistance. The information gained here lays the foundation for mapping out the complete KSM biosynthetic pathway.


  • Organizational Affiliation

    Genomics Research Center, Academia Sinica, Taipei 115, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative UDP-N-acetylglucosamine 2-epimerase
A, B
384Streptomyces kasugaensisMutation(s): 0 
Gene Names: kasQ
EC: 5.1.3.14
UniProt
Find proteins for A0A0K1H2R6 (Streptomyces kasugaensis)
Explore A0A0K1H2R6 
Go to UniProtKB:  A0A0K1H2R6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K1H2R6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.349α = 90
b = 106.052β = 124.87
c = 94.343γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia Sinica (Taiwan)Taiwan--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2023-06-07
    Changes: Database references, Refinement description, Structure summary
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description