4AD4

Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with glucose-1,3-isofagomine and alpha-1,2- mannobiose

Summary for 4AD4

• Entry DOI: 10.2210/pdb4ad4/pdb
• Related: 4ACY 4ACZ 4AD0 4AD1 4AD2 4AD3 4AD5
• Related PRD ID: PRD_900111
• Descriptor: GLYCOSYL HYDROLASE FAMILY 71, alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose, alpha-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: hydrolase, endomannosidase, glycoside hydrolase, gh99, cazy, enzyme-carbohydrate interaction, mannose glycosidase inhibition
• Biological source: BACTEROIDES XYLANISOLVENS
• Total number of polymer chains: 1
• Total formula weight: 44148.89

Authors

Thompson, A.J.,Williams, R.J.,Hakki, Z.,Alonzi, D.S.,Wennekes, T.,Gloster, T.M.,Songsrirote, K.,Thomas-Oates, J.E.,Wrodnigg, T.M.,Spreitz, J.,Stuetz, A.E.,Butters, T.D.,Williams, S.J.,Davies, G.J. (deposition date: 2011-12-21, release date: 2012-02-01, Last modification date: 2024-05-01)

Primary citation

Thompson, A.J.,Williams, R.J.,Hakki, Z.,Alonzi, D.S.,Wennekes, T.,Gloster, T.M.,Songsrirote, K.,Thomas-Oates, J.E.,Wrodnigg, T.M.,Spreitz, J.,Stutz, A.E.,Butters, T.D.,Williams, S.J.,Davies, G.J.
Structural and Mechanistic Insight Into N-Glycan Processing by Endo-Alpha-Mannosidase.
Proc.Natl.Acad.Sci.USA, 109:781-, 2012

PubMed Abstract: N-linked glycans play key roles in protein folding, stability, and function. Biosynthetic modification of N-linked glycans, within the endoplasmic reticulum, features sequential trimming and readornment steps. One unusual enzyme, endo-α-mannosidase, cleaves mannoside linkages internally within an N-linked glycan chain, short circuiting the classical N-glycan biosynthetic pathway. Here, using two bacterial orthologs, we present the first structural and mechanistic dissection of endo-α-mannosidase. Structures solved at resolutions 1.7-2.1 Å reveal a (β/α)(8) barrel fold in which the catalytic center is present in a long substrate-binding groove, consistent with cleavage within the N-glycan chain. Enzymatic cleavage of authentic Glc(1/3)Man(9)GlcNAc(2) yields Glc(1/3)-Man. Using the bespoke substrate α-Glc-1,3-α-Man fluoride, the enzyme was shown to act with retention of anomeric configuration. Complexes with the established endo-α-mannosidase inhibitor α-Glc-1,3-deoxymannonojirimycin and a newly developed inhibitor, α-Glc-1,3-isofagomine, and with the reducing-end product α-1,2-mannobiose structurally define the -2 to +2 subsites of the enzyme. These structural and mechanistic data provide a foundation upon which to develop new enzyme inhibitors targeting the hijacking of N-glycan synthesis in viral disease and cancer.

PubMed: 22219371
DOI: 10.1073/PNAS.1111482109

Experimental method

X-RAY DIFFRACTION (1.9 Å)