› 2vmf

X-ray diffraction
2.1Å resolution

Structural and biochemical evidence for a boat-like transition state in beta-mannosidases

Released:
DOI: 10.2210/pdb2vmf/pdb
PDB entry 2vmf coloured by chain, front view.
PDB entry 2vmf coloured by chain, side view.
PDB entry 2vmf coloured by chain, top view.
Source organism: Bacteroides thetaiotaomicron VPI-5482
Primary publication:
Structural and biochemical evidence for a boat-like transition state in beta-mannosidases.
Tailford LE, Offen WA, Smith NL, Dumon C, Morland C, Gratien J, Heck MP, Stick RV, Blériot Y, Vasella A, Gilbert HJ, Davies GJ
Nat Chem Biol 4 306-12 (2008)
PMID: 18408714

Function and Biology Details

Reaction catalysed: 
Hydrolysis of terminal, non-reducing beta-D-mannose residues in beta-D-mannosides
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183790 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-mannosidase B Chains: A, B
Molecule details ›
Chains: A, B
Length: 846 amino acids
Theoretical weight: 97.99 KDa
Source organism: Bacteroides thetaiotaomicron VPI-5482
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q8AAK6 (Residues: 26-864; Coverage: 100%)
Gene name: BT_0458
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand MVL 2 x MVL
Ligand EDO 40 x EDO
Ligand BR 16 x BR
Ligand CL 11 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P21
Unit cell:
a: 91.051Å b: 114.663Å c: 99.09Å
α: 90° β: 113.19° γ: 90°
R-values:
R R work R free
0.167 0.164 0.223
Expression system: Escherichia coli BL21

Quick links

Citations

6 review citations

Mechanistic insights into glycosidase chemistry.
Vocadlo et al. (2008)
5 more

3 mentions without citation

Influence of Side Chain Conformation on the Activity of Glycosidase Inhibitors.
Tseng et al. (2023)
2 more