› 4ayp

X-ray diffraction
0.85Å resolution

Structure of The GH47 processing alpha-1,2-mannosidase from Caulobacter strain K31 in complex with thiomannobioside

Released:
DOI: 10.2210/pdb4ayp/pdb
PDB entry 4ayp coloured by chain, front view.
PDB entry 4ayp coloured by chain, side view.
PDB entry 4ayp coloured by chain, top view.
Source organism: Caulobacter sp. K31
Primary publication:
The reaction coordinate of a bacterial GH47 α-mannosidase: a combined quantum mechanical and structural approach.
Thompson AJ, Dabin J, Iglesias-Fernández J, Ardèvol A, Dinev Z, Williams SJ, Bande O, Siriwardena A, Moreland C, Hu TC, Smith DK, Gilbert HJ, Rovira C, Davies GJ
Angew Chem Int Ed Engl 51 10997-1001 (2012)
PMID: 23012075

Function and Biology Details

Reaction catalysed: 
(1a) Man(9)GlcNAc(2)-[protein] + H(2)O = Man(8)GlcNAc(2)-[protein] (isomer 8A(1,2,3)B(1,2)) + beta-D-mannopyranose
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-109212 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Mannosyl-oligosaccharide 1,2-alpha-mannosidase Chain: A
Molecule details ›
Chain: A
Length: 447 amino acids
Theoretical weight: 50.55 KDa
Source organism: Caulobacter sp. K31
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: B0SWV2 (Residues: 27-462; Coverage: 100%)
Gene name: Caul_4035
Sequence domains: Glycosyl hydrolase family 47
Structure domains: Glycosyltransferase

Ligands and Environments

Carbohydrate polymer : NEW Components: Z5L, MAN
Ligand Z5L 1 x Z5L
Ligand MAN 1 x MAN
2 bound ligands:
Ligand CA 2 x CA
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: R3
Unit cell:
a: 144.135Å b: 144.135Å c: 50.301Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.097 0.096 0.106
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

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

5 mentions without citation

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