Rotavirus, the major pathogen of infantile gastroenteritis, carries a nonstructural protein, NSP2, essential for viroplasm formation and genome replication/packaging. In addition to RNA-binding and helix-destabilizing properties, NSP2 exhibits nucleoside triphosphatase activity. A conserved histidine (H225) functions as the catalytic residue for this enzymatic activity, and mutation of this residue abrogates genomic double-stranded RNA synthesis without affecting viroplasm formation. To understand the structural basis of the phosphatase activity of NSP2, we performed crystallographic analyses of native NSP2 and a functionally defective H225A mutant in the presence of nucleotides. These studies showed that nucleotides bind inside a cleft between the two domains of NSP2 in a region that exhibits structural similarity to ubiquitous cellular HIT (histidine triad) proteins. Only minor conformational alterations were observed in the cleft upon nucleotide binding and hydrolysis. This hydrolysis involved the formation of a stable phosphohistidine intermediate. These observations, reminiscent of cellular nucleoside diphosphate (NDP) kinases, prompted us to investigate whether NSP2 exhibits phosphoryl-transfer activity. Bioluminometric assay showed that NSP2 exhibits an NDP kinase-like activity that transfers the bound phosphate to NDPs. However, NSP2 is distinct from the highly conserved cellular NDP kinases in both its structure and catalytic mechanism, thus making NSP2 a potential target for antiviral drug design. With structural similarities to HIT proteins, which are not known to exhibit NDP kinase activity, NSP2 represents a unique example among structure-activity relationships. The newly observed phosphoryl-transfer activity of NSP2 may be utilized for homeostasis of nucleotide pools in viroplasms during genome replication.Rotaviruses are the major cause of life-threatening diarrhea in children worldwide (13). The genome (ϳ18 kb) of rotavirus consists of 11 segments of double-stranded RNA (dsRNA) encoding six structural and six nonstructural proteins (NSPs) (13). Several studies have shown that endogenous transcription of dsRNA segments, genome replication/packaging, and assembly of subviral particles take place in specialized compartments called viroplasms, which appear early during infection (30). NSP2, along with NSP5, is essential for the formation of these perinuclear, non-membrane-bound, electron-dense inclusions (14). Coexpression of NSP2 and NSP5 alone has been shown to be sufficient for the formation of viroplasm-like structures (14). NSP2 also appears to interact directly or indirectly with other structural proteins present in the viroplasm, such as VP2 (30), which forms the innermost capsid layer of the virion (32), and VP1, which is the viral RNA-dependent RNA polymerase (45).Biochemical studies on recombinant NSP2 have shown that in addition to single-stranded-RNA (ssRNA)-binding and helix-destabilizing activities (42), NSP2 exhibits nucleotide triphosphatase (NTPase) activity (40). The protein cleaves...