9XHM

Crystal structure of AcvB from Agrobacterium tumefaciens

Summary for 9XHM

• Entry DOI: 10.2210/pdb9xhm/pdb
• Descriptor: AcvB, 1,2-ETHANEDIOL (2 entities in total)
• Functional Keywords: lysyl-phosphatidylglycerol hydrolase, hydrolase
• Biological source: Agrobacterium tumefaciens
• Total number of polymer chains: 2
• Total formula weight: 93633.51

Authors

Hoshi, M.,Watanabe, Y. (deposition date: 2025-11-01, release date: 2026-04-15, Last modification date: 2026-06-03)

Primary citation

Hoshi, M.,Matsumoto, D.,Watanabe, Y.
Structural basis of substrate recognition and membrane association by the bacterial lysyl-phosphatidylglycerol hydrolase AcvB.
Commun Biol, 9:-, 2026

PubMed Abstract: Bacteria adapt to environmental stresses via membrane phospholipid remodeling; however, the underlying molecular mechanism remains largely elusive. In Agrobacterium tumefaciens, the lysyl-phosphatidylglycerol (Lys-PG) synthase lpiA and periplasmic hydrolase acvB genes form an operon that controls Lys-PG levels. We determined the crystal structures of mature AcvB and its C-terminal catalytic domain at 3.1 Å and 1.8 Å resolution, respectively. The catalytic domain forms a negatively charged cavity that recognizes the positively charged Lys-PG head group through multiple acidic residues, including Asp271, Asp340, and Asp370. A hydrophobic protruding loop containing Trp378 and Leu379 mediates membrane association and contributes to Lys-PG hydrolysis. Further, AcvB interacts with LpiA via its C-terminal domain, suggesting a cooperative module for Lys-PG turnover. These findings reveal the structural basis of Lys-PG hydrolysis and provide mechanistic insight into adaptive lipid modification at the bacterial membrane interface, and may guide future development of antibacterial agents against plant-pathogenic bacteria.

PubMed: 42174249
DOI: 10.1038/s42003-026-10087-1

Experimental method

X-RAY DIFFRACTION (3.13 Å)