7DCK

Crystal structure of phosphodiesterase tw9814

Summary for 7DCK

• Entry DOI: 10.2210/pdb7dck/pdb
• Descriptor: Lactamase_B domain-containing protein, MANGANESE (II) ION (3 entities in total)
• Functional Keywords: phosphodiesterase, manganese, hydrolase
• Biological source: Epsilonproteobacteria bacterium (ex Lamellibrachia satsuma)
• Total number of polymer chains: 2
• Total formula weight: 55214.55

Authors

Heo, Y.,Yun, J.H.,Park, J.H.,Park, S.B.,Cha, S.S.,Lee, W. (deposition date: 2020-10-26, release date: 2021-10-27, Last modification date: 2024-10-30)

Primary citation

Heo, Y.,Park, S.B.,Jeon, Y.E.,Yun, J.H.,Jeong, B.G.,Cha, S.S.,Lee, W.
Structural and functional identification of the uncharacterized metallo-beta-lactamase superfamily protein TW9814 as a phosphodiesterase with unique metal coordination.
Acta Crystallogr D Struct Biol, 78:532-541, 2022

PubMed Abstract: Metallo-β-lactamase (MBL) superfamily proteins have a common αβ/βα sandwich fold and perform a variety of functions through metal-mediated catalysis. However, because of the enormous scale of this superfamily, only a small percentage of the proteins belonging to the superfamily have been annotated structurally or functionally to date. Therefore, much remains unknown about the MBL superfamily proteins. Here, TW9814, a hypothetical MBL superfamily protein, was structurally and functionally investigated. Guided by the crystal structure of dimeric TW9814, it was demonstrated that TW9814 functions as a phosphodiesterase (PDE) in the presence of divalent metal ions such as manganese(II) or nickel(II). A docking model between TW9814 and the substrate bis(p-nitrophenyl)phosphate (bpNPP) showed the importance of the dimerization of TW9814 for its bpNPP-hydrolyzing activity and for the interaction between the enzyme and the substrate. TW9814 showed outstanding catalytic efficiency (k/K) under alkaline conditions compared with other PDEs. The activity of TW9814 appears to be regulated through a disulfide bond, which is a feature that is not present in other MBL superfamily members. This study provides a platform for the functional characterization of other hypothetical proteins of the MBL or other superfamilies.

PubMed: 35362475
DOI: 10.1107/S2059798322002108

Experimental method

X-RAY DIFFRACTION (2.34 Å)