7UJN

Structure of Human SAMHD1 with Non-Hydrolysable dGTP Analog

Summary for 7UJN

• Entry DOI: 10.2210/pdb7ujn/pdb
• EMDB information: 26567
• Descriptor: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1, 2'-deoxyguanosine-5'-O-(1-thiotriphosphate) (2 entities in total)
• Functional Keywords: dntp triphosphatase, hydrolase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 4
• Total formula weight: 295500.62

Authors

Huynh, K.W.,Ammirati, M.,Han, S. (deposition date: 2022-03-31, release date: 2022-07-20, Last modification date: 2024-02-14)

Primary citation

Orris, B.,Huynh, K.W.,Ammirati, M.,Han, S.,Bolanos, B.,Carmody, J.,Petroski, M.D.,Bosbach, B.,Shields, D.J.,Stivers, J.T.
Phosphorylation of SAMHD1 Thr592 increases C-terminal domain dynamics, tetramer dissociation and ssDNA binding kinetics.
Nucleic Acids Res., 50:7545-7559, 2022

PubMed Abstract: SAM and HD domain containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) is driven into its activated tetramer form by binding of GTP activator and dNTP activators/substrates. In addition, the inactive monomeric and dimeric forms of the enzyme bind to single-stranded (ss) nucleic acids. During DNA replication SAMHD1 can be phosphorylated by CDK1 and CDK2 at its C-terminal threonine 592 (pSAMHD1), localizing the enzyme to stalled replication forks (RFs) to promote their restart. Although phosphorylation has only a small effect on the dNTPase activity and ssDNA binding affinity of SAMHD1, perturbation of the native T592 by phosphorylation decreased the thermal stability of tetrameric SAMHD1 and accelerated tetramer dissociation in the absence and presence of ssDNA (∼15-fold). In addition, we found that ssDNA binds competitively with GTP to the A1 site. A full-length SAMHD1 cryo-EM structure revealed substantial dynamics in the C-terminal domain (which contains T592), which could be modulated by phosphorylation. We propose that T592 phosphorylation increases tetramer dynamics and allows invasion of ssDNA into the A1 site and the previously characterized DNA binding surface at the dimer-dimer interface. These features are consistent with rapid and regiospecific inactivation of pSAMHD1 dNTPase at RFs or other sites of free ssDNA in cells.

PubMed: 35801923
DOI: 10.1093/nar/gkac573

Experimental method

ELECTRON MICROSCOPY (2.89 Å)