A.baumannii Uncharacterized sugar kinase ydjH

Experimental Data Snapshot

  • Resolution: 3.04 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.274 

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Structure of YdjH from Acinetobacter baumannii revealed an active site of YdjH family sugar kinase.

Lee, G.H.Kim, J.H.Ha, H.J.Park, H.H.

(2023) Biochem Biophys Res Commun 664: 27-34

  • DOI: https://doi.org/10.1016/j.bbrc.2023.04.073
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Bacterial sugar kinase is a central enzyme for proper sugar degradation in bacteria, essential for survival and growth. Therefore, this enzyme family is a primary target for antibacterial drug development, with YdjH most preferring to phosphorylate higher-order monosaccharides with a carboxylate terminus. Sugar kinases express diverse specificity and functions, making specificity determination of this family a prominent issue. This study examines the YdjH crystal structure from Acinetobacter baumannii (abYdjH), which has an exceptionally high antibiotic resistance and is considered a superbug. Our structural and biochemical study revealed that abYdjH has a widely open lid domain and is a solution dimer. In addition, the putative active site of abYdjH was determined based on structural analysis, sequence comparison, and in silico docking. Finally, we proposed the active site-forming residues that determine various sugar specificities from abYdjH. This study contributes towards a deeper understanding of the phosphorylation process and bacterial sugar metabolism of YdjH family to design the next-generation antibiotics for targeting A. baumannii.

  • Organizational Affiliation

    College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea; Department of Global Innovative Drugs, Graduate School of Chung-Ang University, Seoul, 06974, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized sugar kinase YdjH
A, B
332Acinetobacter baumanniiMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.04 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.274 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.43α = 90
b = 84.3β = 90
c = 161.06γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection