Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

 

Sterile α-motif/histidine-aspartate domain-containing protein (SAMHD1) is a homo-tetrameric GTP/dGTP-activated dNTPase which ​catalyses the conversion of dNTP into 2'-deoxynucleoside and triphosphate. The enzyme interconverts between an inactive monomeric or dimeric form and a dGTP/GTP-induced active tetrameric form. SAMHD1 is ubiquitously expressed in various human organs.

SAMHD1 plays an important role in human innate immunity, autoimmunity and cell cycle control. It blocks retroviral infections (including HIV) and transposition of endogenous retroelements as well as preventing infections from certain DNA viruses.

 

Reference Protein and Structure

Sequence
Q9Y3Z3 UniProt (3.1.5.-) (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
4bzc - Crystal structure of the tetrameric dGTP-bound wild type SAMHD1 catalytic core (2.88 Å) PDBe PDBsum 4bzc
Catalytic CATH Domains
1.10.3210.10 CATHdb (see all for 4bzc)
Cofactors
Iron(3+) (1), Magnesium(2+) (2)
Click To Show Structure

Enzyme Reaction (EC:3.1.5.-)

2'-deoxyribonucleoside 5'-triphosphate(4-)
CHEBI:61560ChEBI
+
water
CHEBI:15377ChEBI
→
2'-deoxyribonucleoside
CHEBI:18274ChEBI
+
hydron
CHEBI:15378ChEBI
+
triphosphate(5-)
CHEBI:18036ChEBI

Enzyme Mechanism

Introduction

In the active configuration, a water molecule bridges an Fe2+ ion and an Mg2+ ion in a bi-metallic centre. This facilitates partial dissociation to hydroxide at neutral pH which then performs a nucleophilic attack at Pα. Inversion at Pα and breakage of the Pα-O5' bond results in incorporation of the hydroxide into the triphosphate product and release of the 2'-deoxynucleoside. His215 acts to stabilise evolving negative charge and donates a proton to the leaving 2'-deoxynucleoside.

Catalytic Residues Roles

UniProt PDB* (4bzc)
Arg366, Lys312 Arg366(290)A, Lys312(236)A Coordinates γ-phosphate via hydrogen bonds. hydrogen bond donor
Asp311, His167, His206, Asp207 Asp311(235)A, His167(91)A, His206(130)A, Asp207(131)A Coordinated to Fe2+ which is part of the bi-metallic centre. metal ligand
His233 His233(157)A Magnesium coordination by His233 at the Fe-Mg bi-metallic centre is important for dNTP coordination and hydrolysis. The H233A substitution reduced the apparent kcat for GTP-activated dATP hydrolysis by 300-fold. metal ligand
His210 His210(134)A Coordinates α-phosphate of dNTP. hydrogen bond donor
His215 His215(139)A His215 side chain makes a hydrogen bond with the O5' of the 2'-deoxynucleoside. His215 is positioned to stabilise evolving negative charge from ES to EP and protonates the leaving 2'-deoxynucleoside. His215 is also hydrogen-bonded to Asp218 which further contributes to charge neutralisation via proton relay. The H215A mutation abolishes triphosphohydrolase activity. hydrogen bond donor, electrostatic stabiliser, proton donor
Asp218 Asp218(142)A Asp218 is a highly conversed residue that makes a charged hydrogen bond to the side chain of His215, stabilising a positive charge of His215 and facilitating protonation of the O5′ on the 2′-deoxynucleoside leaving group. The D218A mutation reduced the apparent kcat by approximately 40-fold. hydrogen bond acceptor, electrostatic stabiliser
Asp319, Gln149 Asp319(243)A, Gln149(73)A The side chains of Asp319 and Gln149 form hydrogen bonds to the 3' OH group on the 2'-deoxyribose. hydrogen bond acceptor
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

bimolecular nucleophilic substitution, proton transfer, assisted tautomerisation (not keto-enol), coordination to a metal ion, overall reactant used, overall product formed, proton relay

References

  1. Morris ER et al. (2020), Nat Commun, 11, 3165-. Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis. DOI:10.1038/s41467-020-16983-2. PMID:32576829.
  2. Morris ER et al. (2021), Biochemistry, 60, 1682-1698. Probing the Catalytic Mechanism and Inhibition of SAMHD1 Using the Differential Properties of Rp- and Sp-dNTPαS Diastereomers. DOI:10.1021/acs.biochem.0c00944. PMID:33988981.
  3. Li Y et al. (2015), J Biol Chem, 290, 29428-29437. Structural Insights into the High-efficiency Catalytic Mechanism of the Sterile α-Motif/Histidine-Aspartate Domain-containing Protein. DOI:10.1074/jbc.M115.663658. PMID:26438820.

Step 1. The hydroxide formed by coordination in the bimetallic centre performs a nucleophilic attack at Pα, inducing breakage of the Pα-O5' bond. His215 protonates the 2'-deoxynucleoside leaving group.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp311(235)A metal ligand
His167(91)A metal ligand
His206(130)A metal ligand
Asp207(131)A metal ligand
His233(157)A metal ligand
His215(139)A proton donor
Arg366(290)A hydrogen bond donor
Lys312(236)A hydrogen bond donor
His210(134)A hydrogen bond donor
His215(139)A hydrogen bond donor
Gln149(73)A hydrogen bond donor
Asp218(142)A hydrogen bond acceptor
Asp319(243)A hydrogen bond acceptor
His215(139)A electrostatic stabiliser
Asp218(142)A electrostatic stabiliser

Chemical Components

ingold: bimolecular nucleophilic substitution, proton transfer, assisted tautomerisation (not keto-enol), coordination to a metal ion, overall reactant used, overall product formed, proton relay
Download: Image, Marvin File

Step 1. The hydroxide formed by coordination in the bimetallic centre performs a nucleophilic attack at Pα, inducing breakage of the Pα-O5' bond. His215 protonates the 2'-deoxynucleoside leaving group.

Products.

Contributors

Noa Marson, Antonio Ribeiro