Heparan sulfate glucosamine 3-O-sulfotransferase

 

3-O-sulfotransferase (3-OST) is one of the enzymes involved in the biosynthesis of heparan sulfate by catalyzing the transfer of a sulfate group from 3'-phosphoadenosine-5'-phosphosulfate to glucosamine units of heparan sulfate. Heparan sulfates are polysaccharides with variable patterns of sulfation and acetylation that serve as entry receptors for herpes simplex virus type 1 (HSV-1). Therefore, this enzyme might be a target for drugs since its inhibition may lead to the blockage of HSV-1 viral infections.

 

Reference Protein and Structure

Sequence
Q9Y663 UniProt (2.8.2.30) IPR037359 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1t8u - Crystal Structure of human 3-O-Sulfotransferase-3 with bound PAP and tetrasaccharide substrate (1.95 Å) PDBe PDBsum 1t8u
Catalytic CATH Domains
3.40.50.300 CATHdb (see all for 1t8u)
Click To Show Structure

Enzyme Reaction (EC:2.8.2.30)

3'-phosphonato-5'-adenylyl sulfate(4-)
CHEBI:58339ChEBI
+
heparan sulfate alpha-D-glucosaminide polyanion
CHEBI:58388ChEBI
→
heparan sulfate alpha-D-glucosaminide 3-sulfate polyanion
CHEBI:70975ChEBI
+
adenosine 3',5'-bismonophosphate(4-)
CHEBI:58343ChEBI
+
hydron
CHEBI:15378ChEBI
Alternative enzyme names: Glucosaminyl 3-O-sulfotransferase 3(a), 3(b), Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A, Isoform/isozyme 3(a) and 3(b) (3-OST-3(A), 3-OST-3(B), HS3ST3A, HS3ST3B), Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3, Glucosaminyl 3-O-sulfotransferase 3, 3-OST-3,

Enzyme Mechanism

Introduction

The reaction mechanism of heparan sulfate glucosamine 3-O-sulfotransferase occurs through a single SN2 reaction step. Active site configurations with a positively charged His186 and negatively charged Asp189 and Glu184 are the most energetically favourable, according to computational experiments. Glu184 is neutral due to proton transfer from Lys215. Glu184 side chain carbonyl oxygen deprotonates 3-OH, resulting in a nucleophilic attack of the 3-O group towards the sulfate group of 3' phosphoadenosine 5'-phosphosulfate. A proton from Glu184 is transferred back to Lys215, to accommodate for the transfer of the proton from O3.

Catalytic Residues Roles

UniProt PDB* (1t8u)
Asp189 Asp189(55)A Asp189 deprotonates His186, resulting in the initiation of the proton relay system. hydrogen bond acceptor, electrostatic stabiliser
His186 His186(52)A His186 involves in proton relay system for donating and accepting protons from other catalytic residues, Asp189 and Glu184. hydrogen bond donor, electrostatic stabiliser
Glu184 Glu184(50)A Acts as a general acid/base to activate the nucleophilic attacks of the 3'-O position of glucosamine units towards the sulfate group of the 3'-phosphoadenosine 5'-phosphosulfate. hydrogen bond acceptor, hydrogen bond donor, proton acceptor
Lys162 Lys162(28)A During the formation of the products, one proton from the Lys162 amine group was fully transferred to an oxygen atom of the PAP phosphate group, thus stabilizing the leaving phosphate. electrostatic stabiliser, proton donor
Lys215, Lys162, Lys368 Lys215(81)A, Lys162(28)A, Lys368(234)A The active site negative charge is stabilized by the presence of the three lysine residues Lys162, Lys215 and Lys368. These residues form hydrogen bonds with both PAPS and the catalytic Glu184. hydrogen bond acceptor, electrostatic stabiliser
*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

proton transfer, overall product formed, overall reactant used, bimolecular nucleophilic substitution

References

  1. Sousa RP et al. (2016), Phys Chem Chem Phys, 18, 11488-11496. Insights into the reaction mechanism of 3-O-sulfotransferase through QM/MM calculations. DOI:10.1039/c5cp06224a. PMID:27063019.
  2. Moon AF et al. (2004), J Biol Chem, 279, 45185-45193. Structural analysis of the sulfotransferase (3-o-sulfotransferase isoform 3) involved in the biosynthesis of an entry receptor for herpes simplex virus 1. DOI:10.1074/jbc.m405013200. PMID:15304505.
  3. Berman HM et al. (2000), Nucleic Acids Res, 28, 235-242. The Protein Data Bank. DOI:10.1093/nar/28.1.235. PMID:10592235.

Step 1. The Glu184 side chain carbonyl oxygen deprotonates 3-OH, resulting in a nucleophilic attack of 3-O towardsthe sulfate group of 3' phosphoadenosine 5'-phosphosulfate. Regeneration of the protonation states of Glu184 and Lys162 occurs probably with the solvation of the active site after the substrate has left.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu184(50)A proton acceptor
Lys162(28)A electrostatic stabiliser
His186(52)A electrostatic stabiliser
Asp189(55)A electrostatic stabiliser
Lys368(234)A electrostatic stabiliser, hydrogen bond donor
Glu184(50)A hydrogen bond acceptor
Lys215(81)A hydrogen bond acceptor
Glu184(50)A hydrogen bond donor
His186(52)A hydrogen bond donor
Asp189(55)A hydrogen bond acceptor
Lys215(81)A electrostatic stabiliser
Lys162(28)A proton donor

Chemical Components

proton transfer, overall product formed, overall reactant used, ingold: bimolecular nucleophilic substitution
Download: Image, Marvin File

Step 1. The Glu184 side chain carbonyl oxygen deprotonates 3-OH, resulting in a nucleophilic attack of 3-O towardsthe sulfate group of 3' phosphoadenosine 5'-phosphosulfate. Regeneration of the protonation states of Glu184 and Lys162 occurs probably with the solvation of the active site after the substrate has left.

Products.

Contributors

Trung Nguyen, Marko Babić, Antonio Ribeiro