› 4v27

X-ray diffraction
1.9Å resolution

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-isofagomine

Released:
DOI: 10.2210/pdb4v27/pdb
PDB entry 4v27 coloured by chain, front view.
PDB entry 4v27 coloured by chain, side view.
PDB entry 4v27 coloured by chain, top view.
Source organism: Bacteroides xylanisolvens XB1A
Primary publication:
Structural and kinetic dissection of the endo-α-1,2-mannanase activity of bacterial GH99 glycoside hydrolases from Bacteroides spp.
Hakki Z, Thompson AJ, Bellmaine S, Speciale G, Davies GJ, Williams SJ
Chemistry 21 1966-77 (2015)
PMID: 25487964

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
Macromolecule:
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(DE3)
UniProt:
  • Canonical: D6D1V7 (Residues: 1-380; Coverage: 100%)
Gene name: BXY_34140
Sequence domains: Glycosyl hydrolase family 99
Structure domains: Glycosidases

Ligands and Environments

3 bound ligands:
Ligand MAN 1 x MAN
Ligand IFM 1 x IFM
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH3R
Spacegroup: I4
Unit cell:
a: 108.28Å b: 108.28Å c: 67.62Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.152 0.151 0.188
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Mannoside recognition and degradation by bacteria.
Ladevèze et al. (2017)
10 other articles

1 mention without citation

Structure of human endo-α-1,2-mannosidase (MANEA), an antiviral host-glycosylation target.
Sobala et al. (2020)