› 4ad0

X-ray diffraction
2.09Å resolution

Structure of the GH99 endo-alpha-mannosidase from Bacteriodes thetaiotaomicron in complex with BIS-TRIS-Propane

Released:
DOI: 10.2210/pdb4ad0/pdb
PDB entry 4ad0 coloured by chain, front view.
PDB entry 4ad0 coloured by chain, side view.
PDB entry 4ad0 coloured by chain, top view.
Source organism: Bacteroides thetaiotaomicron VPI-5482
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-183601 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endo-alpha-mannosidase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 382 amino acids
Theoretical weight: 43.26 KDa
Source organism: Bacteroides thetaiotaomicron VPI-5482
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q8A109 (Residues: 1-382; Coverage: 100%)
Gene name: BT_3862
Sequence domains: Glycosyl hydrolase family 99
Structure domains: Glycosidases

Ligands and Environments

2 bound ligands:
Ligand B3P 4 x B3P
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P21
Unit cell:
a: 65.993Å b: 168.428Å c: 72.433Å
α: 90° β: 117.08° γ: 90°
R-values:
R R work R free
0.184 0.181 0.237
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)