Nudix hydrolase

NUDIX hydrolases are a superfamily of hydrolytic enzymes capable of cleaving nucleoside diphosphates linked to x (any moiety), hence their name.[1][2][3][4] The reaction yields nucleoside monophosphate (NMP) plus X-P. Substrates hydrolysed by nudix enzymes comprise a wide range of organic pyrophosphates, including nucleoside di- and triphosphates, dinucleoside and diphosphoinositol polyphosphates, nucleotide sugars and RNA caps, with varying degrees of substrate specificity.[3] Enzymes of the NUDIX superfamily are found in all types of organisms, including eukaryotes, bacteria and archaea.[3]

NUDIX
Structure of MT-ADPRase, a Nudix hydrolase from Mycobacterium tuberculosis
Identifiers
SymbolNUDIX
PfamPF00293
Pfam clanCL0261
InterProIPR000086
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary
NUDIX-like
Crystal structure of NADH pyrophosphatase (1790429) from Escherichia coli k12 at 2.20 a resolution
Identifiers
SymbolNUDIX-like
PfamPF09296
Pfam clanCL0261
InterProIPR015375
SCOP21vk6 / SCOPe / SUPFAM
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary

There are two components to the NUDIX family: the so-called NUDIX fold of a beta sheet with alpha helices on each side and the NUDIX motif which contains catalytic and metal-binding amino acids. The Nudix motif is GXXXXXEXXXXXXXREUXEEXGU where U is isoleucine, leucine or valine, and X is any amino acid. This forms a short helix which (usually) contains the catalytic amino acids. NUDIX hydrolases include Dcp2 of the decapping complex, ADP-ribose diphosphatase, MutT, ADPRase, Ap4A hydrolases, RppH, and many others.[5]

References
  1. Bessman MJ, Frick DN, O'Handley SF (October 1996). "The MutT proteins or "Nudix" hydrolases, a family of versatile, widely distributed, "housecleaning" enzymes". J. Biol. Chem. 271 (41): 25059–62. doi:10.1074/jbc.271.41.25059. PMID 8810257.
  2. Mildvan AS, Xia Z, Azurmendi HF, et al. (January 2005). "Structures and mechanisms of Nudix hydrolases". Arch. Biochem. Biophys. 433 (1): 129–43. doi:10.1016/j.abb.2004.08.017. PMID 15581572.
  3. McLennan AG (January 2006). "The Nudix hydrolase superfamily". Cell. Mol. Life Sci. 63 (2): 123–43. doi:10.1007/s00018-005-5386-7. PMID 16378245. S2CID 30202446.
  4. Carreras-Puigvert, Jordi; Zitnik, Marinka; Jemth, Ann-Sofie; Carter, Megan; Unterlass, Judith E.; Hallström, Björn; Loseva, Olga; Karem, Zhir; Calderón-Montaño, José Manuel; Lindskog, Cecilia; Edqvist, Per-Henrik (2017-11-16). "A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family". Nature Communications. 8 (1): 1541. doi:10.1038/s41467-017-01642-w. ISSN 2041-1723. PMC 5688067. PMID 29142246.
  5. Mildvan, A.S.; Xia, Z.; Azurmendi, H.F.; Saraswat, V.; Legler, P.M.; Massiah, M.A.; Gabelli, S.B.; Bianchet, M.A.; et al. (2005). "Structures and mechanisms of Nudix hydrolases". Archives of Biochemistry and Biophysics. 433 (1): 129–143. doi:10.1016/j.abb.2004.08.017. PMID 15581572.
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