Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the transfer of sulfate to position 6 of non-reducing N-acetylglucosamine (GlcNAc) residues within keratan-like structures on N-linked glycans and within mucin-associated glycans that can ultimately serve as SELL ligands. SELL ligands are present in high endothelial cells (HEVs) and play a central role in lymphocyte homing at sites of inflammation. Participates in biosynthesis of the SELL ligand sialyl 6-sulfo Lewis X and in lymphocyte homing to Peyer patches. Has no activity toward O-linked sugars. Its substrate specificity may be influenced by its subcellular location. Sulfates GlcNAc residues at terminal, non-reducing ends of oligosaccharide chains. 3'-phosphoadenylyl sulfate + 3-O-{N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl}-L-threonyl-[protein] = 3-O-{6-O-sulfo-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl}-L-threonyl-[protein] + adenosine 3',5'-bisphosphate + H(+) 3'-phosphoadenylyl sulfate + 3-O-{N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl}-L-seryl-[protein] = 3-O-{6-O-sulfo-N-acetyl-beta-D-glucosaminyl-(1->3)-beta-D-galactosyl-(1->3)-N-acetyl-alpha-D-galactosaminyl}-L-seryl-[protein] + adenosine 3',5'-bisphosphate + H(+) 3'-phosphoadenylyl sulfate + 3-O-{beta-D-galactosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl}-L-threonyl-[protein] = 3-O-{beta-D-galactosyl-(1->3)-[6-O-sulfo-N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl}-L-threonyl-[protein] + adenosine 3',5'-bisphosphate + H(+) 3'-phosphoadenylyl sulfate + 3-O-{beta-D-galactosyl-(1->3)-[N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl}-L-seryl-[protein] = 3-O-{beta-D-galactosyl-(1->3)-[6-O-sulfo-N-acetyl-beta-D-glucosaminyl-(1->6)]-N-acetyl-alpha-D-galactosaminyl}-L-seryl-[protein] + adenosine 3',5'-bisphosphate + H(+) Protein modification; carbohydrate sulfation. Homodimer; disulfide-linked. Homodimerization is not essential for enzyme activity. Widely expressed. Highly expressed in bone marrow, peripheral blood leukocytes, spleen, brain, spinal cord, ovary and placenta. Expressed by high endothelial cells (HEVs) and leukocytes. Up-regulated upon cytokine activation. Glycosylation at Asn-475 is required for catalytic activity. Higher levels of expression compared to isoform 1 when expressed in HeLa cells. Exhibits similar intracellular GlcNAc-6-O-sulfation activity. Belongs to the sulfotransferase 1 family. Gal/GlcNAc/GalNAc subfamily.