› 4ad5

X-ray diffraction
1.9Å resolution

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

Released:
DOI: 10.2210/pdb4ad5/pdb
PDB entry 4ad5 coloured by chain, front view.
PDB entry 4ad5 coloured by chain, side view.
PDB entry 4ad5 coloured by chain, top view.
Source organism: Bacteroides xylanisolvens XB1A
Primary publication:
Structural and mechanistic insight into N-glycan processing by endo-α-mannosidase.
Thompson AJ, Williams RJ, Hakki Z, Alonzi DS, Wennekes T, Gloster TM, Songsrirote K, Thomas-Oates JE, Wrodnigg TM, Spreitz J, Stütz AE, Butters TD, Williams SJ, Davies GJ
Proc Natl Acad Sci U S A 109 781-6 (2012)
PMID: 22219371

Function and Biology Details

Reaction catalysed: 
GlcMan(9)GlcNAc(2)-[protein] + H(2)O = Man(8)GlcNAc(2)-[protein] (isomer 8A(1,2,3)B(1,2)) + alpha-D-glucosyl-(1->3)-alpha-D-mannopyranose
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112767 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Glycosyl hydrolase family 71 Chain: A
Molecule details ›
Chain: A
Length: 380 amino acids
Theoretical weight: 43.48 KDa
Source organism: Bacteroides xylanisolvens XB1A
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: D6D1V7 (Residues: 1-380; Coverage: 100%)
Gene name: BXY_34140
Sequence domains: Glycosyl hydrolase family 99
Structure domains: Glycosidases

Ligands and Environments

Carbohydrate polymer : NEW Components: MAN
Carbohydrate polymer
2 bound ligands:
Ligand GLC 1 x GLC
Ligand DMJ 1 x DMJ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: I4
Unit cell:
a: 108.844Å b: 108.844Å c: 67.762Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.161 0.158 0.205
Expression system: Escherichia coli BL21

Quick links

Citations

5 review citations

Dissecting conformational contributions to glycosidase catalysis and inhibition.
Speciale et al. (2014)
4 more

1 mention without citation

Structural and mechanistic insight into N-glycan processing by endo-α-mannosidase.
Thompson et al. (2012)