5KDU

ZmpB metallopeptidase in complex with a2,6-Sialyl T-antigen

Summary for 5KDU

• Entry DOI: 10.2210/pdb5kdu/pdb
• Related: 5KD2 5KD5 5KD8 5KDJ 5KDN 5KDS 5KDV 5KDW 5KDX
• Descriptor: F5/8 type C domain protein, beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose, 1,2-ETHANEDIOL, ... (6 entities in total)
• Functional Keywords: glycopeptidase, o-glycan, pf13402, hydrolase
• Biological source: Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)
• Total number of polymer chains: 1
• Total formula weight: 61484.57

Authors

Noach, I.,Ficko-Blean, E.,Stuart, C.,Boraston, A.B. (deposition date: 2016-06-08, release date: 2017-01-11, Last modification date: 2023-09-27)

Primary citation

Noach, I.,Ficko-Blean, E.,Pluvinage, B.,Stuart, C.,Jenkins, M.L.,Brochu, D.,Buenbrazo, N.,Wakarchuk, W.,Burke, J.E.,Gilbert, M.,Boraston, A.B.
Recognition of protein-linked glycans as a determinant of peptidase activity.
Proc. Natl. Acad. Sci. U.S.A., 114:E679-E688, 2017

PubMed Abstract: The vast majority of proteins are posttranslationally altered, with the addition of covalently linked sugars (glycosylation) being one of the most abundant modifications. However, despite the hydrolysis of protein peptide bonds by peptidases being a process essential to all life on Earth, the fundamental details of how peptidases accommodate posttranslational modifications, including glycosylation, has not been addressed. Through biochemical analyses and X-ray crystallographic structures we show that to hydrolyze their substrates, three structurally related metallopeptidases require the specific recognition of O-linked glycan modifications via carbohydrate-specific subsites immediately adjacent to their peptidase catalytic machinery. The three peptidases showed selectivity for different glycans, revealing protein-specific adaptations to particular glycan modifications, yet always cleaved the peptide bond immediately preceding the glycosylated residue. This insight builds upon the paradigm of how peptidases recognize substrates and provides a molecular understanding of glycoprotein degradation.

PubMed: 28096352
DOI: 10.1073/pnas.1615141114

Experimental method

X-RAY DIFFRACTION (2 Å)