8IWL

A.baumannii Uncharacterized sugar kinase ydjH

Summary for 8IWL

• Entry DOI: 10.2210/pdb8iwl/pdb
• Descriptor: Uncharacterized sugar kinase YdjH (1 entity in total)
• Functional Keywords: sugar kinase, atpase, sugar binding protein
• Biological source: Acinetobacter baumannii
• Total number of polymer chains: 2
• Total formula weight: 73169.41

Authors

Lee, G.H.,Park, H.H. (deposition date: 2023-03-30, release date: 2023-05-24, Last modification date: 2024-05-29)

Primary citation

Lee, G.H.,Kim, J.H.,Ha, H.J.,Park, H.H.
Structure of YdjH from Acinetobacter baumannii revealed an active site of YdjH family sugar kinase.
Biochem.Biophys.Res.Commun., 664:27-34, 2023

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.

PubMed: 37130458
DOI: 10.1016/j.bbrc.2023.04.073

Experimental method

X-RAY DIFFRACTION (3.04 Å)