› 4acy

X-ray diffraction
1.69Å resolution

Selenomethionine derivative of the GH99 endo-alpha-mannosidase from Bacteroides thetaiotaomicron

Released:
DOI: 10.2210/pdb4acy/pdb
PDB entry 4acy coloured by chain, front view.
PDB entry 4acy coloured by chain, side view.
PDB entry 4acy 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
Molecule details ›
Chains: A, B
Length: 382 amino acids
Theoretical weight: 43.64 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 GOL 7 x GOL
Ligand FMT 2 x FMT
1 modified residue:
Ligand MSE 16 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P1
Unit cell:
a: 47.721Å b: 60.002Å c: 78.666Å
α: 103.45° β: 102.59° γ: 98.59°
R-values:
R R work R free
0.177 0.175 0.208
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

2 mentions without citation

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