6B9V

Crystal Structure of a New Diphosphatase from the PhnP Family

Summary for 6B9V

• Entry DOI: 10.2210/pdb6b9v/pdb
• Descriptor: Beta-lactamase-like protein, MANGANESE (II) ION, PHOSPHATE ION, ... (5 entities in total)
• Functional Keywords: metallo-beta-lactamase-like hydrolase, diphosphatase, hydrolase
• Biological source: Koribacter versatilis (strain Ellin345)
• Total number of polymer chains: 2
• Total formula weight: 61774.48

Authors

Li, Q.,Bruner, S.D. (deposition date: 2017-10-11, release date: 2018-10-17, Last modification date: 2023-10-04)

Primary citation

Beaudoin, G.A.W.,Li, Q.,Bruner, S.D.,Hanson, A.D.
An unusual diphosphatase from the PhnP family cleaves reactive FAD photoproducts.
Biochem.J., 475:261-272, 2018

PubMed Abstract: Flavins are notoriously photolabile, but while the photoproducts derived from the -alloxazine ring are well known the other photoproducts are not. In the case of FAD, typically the main cellular flavin, the other photoproducts are predicted to include four- and five-carbon sugars linked to ADP. These FAD photoproducts were shown to be potent glycating agents, more so than ADP-ribose. Such toxic compounds would require disposal via an ADP-sugar diphosphatase or other route. Comparative analysis of bacterial genomes uncovered a candidate disposal gene that is chromosomally clustered with genes for FAD synthesis or transport and is predicted to encode a protein of the PhnP cyclic phosphodiesterase family. The representative PhnP family enzyme from (here named Fpd, AD hotoproduct iphosphatase) was found to have high, Mn-dependent diphosphatase activity against FAD photoproducts, FAD, and ADP-ribose, but almost no phosphodiesterase activity against riboflavin 4',5'-cyclic phosphate, a chemical breakdown product of FAD. To provide a structural basis of the unique Fpd activity, the crystal structure of Fpd was determined. The results place Fpd in the broad metallo-β-lactamase-like family of hydrolases, a diverse family commonly using two metals for hydrolytic catalysis. The active site of Fpd contains two Mn ions and a bound phosphate, consistent with a diphosphatase mechanism. Our results characterize the first PhnP family member that is a diphosphatase rather than a cyclic phosphodiesterase and suggest its involvement in a cellular damage-control system that efficiently hydrolyzes the reactive, ADP-ribose-like products of FAD photodegradation.

PubMed: 29229761
DOI: 10.1042/BCJ20170817

Experimental method

X-RAY DIFFRACTION (1.88 Å)