NudT16

Introduction

NudT16 is a member of the Nudix superfamily of hydrolases which breaks a phosphorus-oxygen bond between the two phosphates in nucleoside diphosphate-linked to moiety X molecules resulting in a nucleoside monophosphate (NMP) and a phosphate linked to moiety X. While NudT16 was initially described as a nuclear RNA and cytoplasmic mRNA decapping enzyme, further studies have shown that it also effectively hydrolyzes inosine diphosphate (IDP) and its hazardous deoxyribose cognate (dIDP) into inosine monophosphate (IMP) and deoxy inosine monophosphate (dIMP), respectively ^[1]. NudT16 has also been shown to regulate levels of 53BP1, an adaptor protein that recruits other proteins to the site of a DNA breakage, through hydrolytic removal of ADP-ribose (ADPr) from Poly-ADP-ribosylated 53BP1 ^[2].

Structure

is a homodimer, consisting of two monomers of the same sequence. A structure on the right shows the hydrolase (one monomer in cyan and the other in purple) in complex with diADPr. This dimerization allows for each subunit to have a deeper . Each monomer consists of two beta-sheets surrounded by alpha-helices, as per the canonical Nudix fold. One beta-sheet is composed entirely of antiparallel strands, while the other has two central parallel strands sandwiched between two outer anti-parallel strands. The catalytically relevant Nudix box characteristic of Nudix hydrolases consists of 23 highly conserved residues (G₁Z_2-6E₇Z_8-14R₁₅E₁₆U₁₇Z₁₈E₁₉E₂₀Z₂₁G₂₂U₂₃ where Z is any amino acid and U is an aliphatic and hydrophobic residue) in a loop-helix-loop region. The Nudix boxes in NudT16 (GARRLELGEALALGSGWRHVCHA) are shown in light pink and dark blue. The Glu residues in the Nudix box play a role in metal ion chelation essential to substrate binding and in the deprotonation of a water molecule to form a hydroxide nucleophile. In contrast to the negatively charged pockets where metal ligands chelate, the adenosine binding pocket is positively charged. The mouth of the binding site is about 9Å in width. Contrary to Nudix ADPRases, Homo sapien NudT16 (HsNudT16) binds adenosine of ADPr and buries it deep in the core, while leaving the non-adenosine ribose exposed to the surface. This orientation allows the exposed ribose to conjugate another protein. ^[3] Many in the mouth of this binding pocket are also involved in hydrogen bonding, the binding of metal ligands, and serve to delimit the binding site.

Function

HsNudT16 has a variety of functions including hydrolysis of certain biomolecules and keeping the cell free of harmful nucleotides. It is responsible for hydrolyzing inosine triphosphate or diphosphate. This protein also has a large substrate specificity and has mRNA decapping capability. Thirawatananond et. al. investigated whether the widening of the ADPr binding site would allow for increased hydrolysis activity by NudT16. The group designed such mutants (F36A, F61S, and a double mutant with both F36A and F61S) and found that for these mutants, NudT16 hydrolysis activity decreased in free ADPr, remained comparably efficient in mono(ADP-ribosylated) proteins, and increased in poly(ADP-ribosylated) proteins. NudT16 is a (Deoxy)inosine diphosphatase. Iyama et. al. found that HsNudT16 binds strongly to GTP, ITP, and XTP. The loss of this protein is followed by increased accumulation of single-strand breaks in DNA, reduced proliferation, and increased cell arrest. They also found increased levels of inosine in RNA, which informed the conclusion that HsNudT16 functions in the nucleus to protect the cell from ITP and its detrimental effects. ^[4]

Relevance

Nudix enzymes are found in every organism in the three domains of life, signifying the importance of phosphodiester bond hydrolysis. ^[5] One of the most biologically important processes NudT16 plays a role in is ADP ribosylation, a post-translational modification that can change various amino acids by conjugating the ADP ribose with the protein. HsNudT16 can reverse ADP ribosylation through hydrolysis of inosine triphosphate or diphosphate. NudT16 plays a crucial role in the cell cycle as its absence in HeLa MR cells caused cell arrest during the S phase.