title: The Nudix hydrolase CDP-chase, a CDP-choline pyrophosphatase, is an asymmetric dimer with two distinct enzymatic activities.
abstract: A Nudix enzyme from Bacillus cereus (NCBI RefSeq accession no. NP_831800) catalyzes the hydrolysis of CDP-choline to produce CMP and phosphocholine. Here, we show that in addition, the enzyme has a 3'→5' RNA exonuclease activity. The structure of the free enzyme, determined to a 1.8-Å resolution, shows that the enzyme is an asymmetric dimer. Each monomer consists of two domains, an N-terminal helical domain and a C-terminal Nudix domain. The N-terminal domain is placed relative to the C-terminal domain such as to result in an overall asymmetric arrangement with two distinct catalytic sites: one with an "enclosed" Nudix pyrophosphatase site and the other with a more open, less-defined cavity. Residues that may be important for determining the asymmetry are conserved among a group of uncharacterized Nudix enzymes from Gram-positive bacteria. Our data support a model where CDP-choline hydrolysis is catalyzed by the enclosed Nudix site and RNA exonuclease activity is catalyzed by the open site. CDP-Chase is the first identified member of a novel Nudix family in which structural asymmetry has a profound effect on the recognition of substrates.
authors.affiliation: Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
authors.forename: Krisna C
authors.initials: KC
authors.lastname: Duong-Ly
authors.forename: Sandra B
authors.initials: SB
authors.lastname: Gabelli
authors.forename: Wenlian
authors.initials: W
authors.lastname: Xu
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Dunn
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Schoeffield
authors.forename: Maurice J
authors.initials: MJ
authors.lastname: Bessman
authors.forename: L Mario
authors.initials: LM
authors.lastname: Amzel
mesh_terms: D000595:Amino Acid Sequence; D001409:Bacillus cereus / Q000201:enzymology; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D003566:Cytidine Diphosphate Choline / Q000378:metabolism; D005092:Exonucleases / Q000737:chemistry* / Q000378:metabolism*; D016253:Microscopy, Immunoelectron; D008958:Models, Molecular; D008969:Molecular Sequence Data; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D011755:Pyrophosphatases / Q000737:chemistry* / Q000378:metabolism*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D000096964:Nudix Hydrolases
chemical_list: D003566:Cytidine Diphosphate Choline; D005092:Exonucleases; D011755:Pyrophosphatases; D000096964:Nudix Hydrolases