6AEM

Crystal structure of the PKD1 domain of Vibrio anguillarum Epp

Summary for 6AEM

• Entry DOI: 10.2210/pdb6aem/pdb
• Descriptor: PKD domain, CALCIUM ION, ZINC ION, ... (4 entities in total)
• Functional Keywords: protease, polycystic kidney disease domain, unknown function
• Biological source: Vibrio anguillarum
• Total number of polymer chains: 2
• Total formula weight: 19285.38

Authors

Ma, Q.,Li, P. (deposition date: 2018-08-05, release date: 2018-12-12, Last modification date: 2023-11-22)

Primary citation

Li, P.,Zang, K.,Li, Y.,Liu, C.,Ma, Q.
Structural basis for specific calcium binding by the polycystic-kidney-disease domain of Vibrio anguillarum protease Epp
Biochem. Biophys. Res. Commun., 505:471-477, 2018

PubMed Abstract: Extracellular proteases are often produced as pre-pro-enzyme and then undergo multiple processing steps to mature into the active form. The protease Epp, a virulent factor of Vibrio anguillarum, belongs to this family. Its maturation might be regulated by Ca via its polycystic kidney disease (PKD) domain, but the molecular mechanism is unknown. Herein, we report the crystal structure of the first PKD domain from V. anguillarum Epp (Epp-PKD1) and its specific Ca-binding capacity. Epp-PKD1 exists as a monomer, consisting of seven β-strands which form two β-sheets stacking with each other. One Ca is bound by the residues Asn3, Gln4, Asp27, Asp29, Asp68 and a water molecule with a pentagonal bipyramidal geometry. Incubating the apo Epp-PKD1 with Ca but not Mg, Mn, or Zn, enhances the thermal and chemical stability of Epp-PKD1, indicating its specific binding to Ca. Epp-PKD1 shares high similarity in both sequence and overall structure with that of Vibrio cholerae PrtV, a homologous protease of Epp, however, they differ in the oligomeric state and local structure at the Ca-binding site, suggesting maturation of PrtV and Epp might be differently regulated by Ca. Likely, proteases may take advantage of the structural diversity in PKD domains to tune their Ca-regulated maturation process.

PubMed: 30268503
DOI: 10.1016/j.bbrc.2018.09.108

Experimental method

X-RAY DIFFRACTION (1.272 Å)