Structural and functional identification of the uncharacterized metallo-β-lactamase superfamily protein TW9814 as a phosphodiesterase with unique metal coordination

Yunseok Heo, Soo Bong Park, Ye Eun Jeon, Ji Hye Yun, Bo Gyeong Jeong, Sun Shin Cha, Weontae Lee

Research output: Contribution to journalArticlepeer-review

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 cat/K m) 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.

Original languageEnglish
Pages (from-to)532-541
Number of pages10
JournalActa Crystallographica Section D: Structural Biology
Volume78
DOIs
StatePublished - 1 Apr 2022

Keywords

  • crystal structure
  • metal coordination
  • metallo-lactamase domains
  • phosphodiesterases.
  • TW9814 hypothetical protein
  • uncharacterized proteins

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