5A58

The structure of GH101 D764N mutant from Streptococcus pneumoniae TIGR4 in complex with serinyl T-antigen

Summary for 5A58

• Entry DOI: 10.2210/pdb5a58/pdb
• Related: 5A55 5A56 5A57 5A59 5A5A
• Related PRD ID: PRD_900084
• Descriptor: ENDO-ALPHA-GALACTOSAMINIDASE, beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose, SERINE, ... (8 entities in total)
• Functional Keywords: hydrolase, endo-beta-n-acetylgalactosaminidase, glycoside hydrolase family 101, gh101, t-antigen, mucin degradation
• Biological source: STREPTOCOCCUS PNEUMONIAE
• Cellular location: Secreted, cell wall ; Peptidoglycan-anchor : Q2MGH6
• Total number of polymer chains: 1
• Total formula weight: 128628.88

Authors

Gregg, K.J.,Suits, M.D.L.,Deng, L.,Vocadlo, D.J.,Boraston, A.B. (deposition date: 2015-06-16, release date: 2015-09-02, Last modification date: 2024-05-08)

Primary citation

Gregg, K.J.,Suits, M.D.L.,Deng, L.,Vocadlo, D.J.,Boraston, A.B.
Structural Analysis of a Family 101 Glycoside Hydrolase in Complex with Carbohydrates Reveals Insights Into its Mechanism.
J.Biol.Chem., 290:25657-, 2015

PubMed Abstract: O-Linked glycosylation is one of the most abundant post-translational modifications of proteins. Within the secretory pathway of higher eukaryotes, the core of these glycans is frequently an N-acetylgalactosamine residue that is α-linked to serine or threonine residues. Glycoside hydrolases in family 101 are presently the only known enzymes to be able to hydrolyze this glycosidic linkage. Here we determine the high-resolution structures of the catalytic domain comprising a fragment of GH101 from Streptococcus pneumoniae TIGR4, SpGH101, in the absence of carbohydrate, and in complex with reaction products, inhibitor, and substrate analogues. Upon substrate binding, a tryptophan lid (residues 724-WNW-726) closes on the substrate. The closing of this lid fully engages the substrate in the active site with Asp-764 positioned directly beneath C1 of the sugar residue bound within the -1 subsite, consistent with its proposed role as the catalytic nucleophile. In all of the bound forms of the enzyme, however, the proposed catalytic acid/base residue was found to be too distant from the glycosidic oxygen (>4.3 Å) to serve directly as a general catalytic acid/base residue and thereby facilitate cleavage of the glycosidic bond. These same complexes, however, revealed a structurally conserved water molecule positioned between the catalytic acid/base and the glycosidic oxygen. On the basis of these structural observations we propose a new variation of the retaining glycoside hydrolase mechanism wherein the intervening water molecule enables a Grotthuss proton shuttle between Glu-796 and the glycosidic oxygen, permitting this residue to serve as the general acid/base catalytic residue.

PubMed: 26304114
DOI: 10.1074/JBC.M115.680470

Experimental method

X-RAY DIFFRACTION (1.8 Å)