Crystal Structure and Substrate Specificity of the 8-oxo-dGTP Hydrolase NUDT1 from Arabidopsis thaliana

Abstract

This is a repository copy of Crystal structure and substrate specificity of the 8-oxo-dGTP hydrolase NUDT1 from Arabidopsis thaliana.

Functional diversification in the Nudix hydrolase gene family drives sesquiterpene biosynthesis in Rosa × wichurana

“…In the RhNUDX1/GPP complex, the two phosphate groups of GPP make polar contacts with residues H49, Y94, S47, and R34 and the aliphatic chain of GPP sits in a hydrophobic pocket (Figure 6a). Although GPP is bound in the active site, it is not in a position to be hydrolyzed, as suggested by the structure of complexes of AtNUDX1/IPP (Henry et al ., 2018) and AtNUDX1/8‐oxo‐dGTP solved with Mg 2+ bound in the active of the enzymes (Jemth et al ., 2019). Therefore, we turned to molecular modeling to further investigate and understand the substrate discrimination by rose NUDX1 proteins.…”

“…From the newly determined RhNUDX1 crystal structure, we conducted molecular modeling on rose NUDX1 proteins, based on the available crystal structures of AtNUDX1 complexed with 8‐oxo‐dGTP (Jemth et al ., 2019), with IPP (Henry et al ., 2018), and with GPP (Liu et al ., 2018), of E. coli MutT complexed with 8‐oxo‐dGMP (Nakamura et al ., 2010), and of human MTH1 complexed with 8‐oxo‐GMP (Svensson et al ., 2011). Models of others Rose NUDX1 were obtained by structural homology from crystal structures of NUDX1 proteins.…”

“…Five residues that are not conserved and that can account for substrate preferences were identified in the substrate pocket of these proteins, namely, A11, F15, G40, S89, and S91 in AtNUDX1; A18, C22, S47, A96, and F98 in RhNUDX1; and V19, C23, G48, V97, and S99 in RwNUDX1‐2c. In addition, it has been shown in AtNUDX1 that N76 and S89, which are in the binding site pocket, play a role in 8‐oxo‐dGTP hydrolysis (Jemth et al ., 2019). The position corresponding to N76 is conserved in all NUDX studied (Figure S5, N83 in RhNUDX1).…”

“…RwNUDX1‐2c has a valine residue (V97) which is bulkier than the corresponding alanine present in other rose NUDX. We already mentioned that this position was shown to be important for interaction with 8‐oxo‐dGTP in AtNUDX1 (Jemth et al ., 2019). In RwNUDX1‐2c, V97 may render the binding pocket more hydrophobic.…”

Identity and functions of inorganic and inositol polyphosphates in plants

“…Human NUDTs have been shown to hydrolyze polyPs, InsPs and other nucleoside polyphosphates (Lonetti et al, 2011). Plant NUDTs act on a large variety of substrates, including ADP-ribose (Ogawa et al, 2005), nucleotides modified by reactive oxygen species (Jemth et al, 2019), and the alarmone pppGpp (Ito et al, 2012). The large number of NUDTs in Arabidopsis and the diverse substrate specificity of NUDT family members render their contribution to polyP metabolism difficult to assess.…”