› 4utf

X-ray diffraction
1.3Å resolution

Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with mannose-alpha-1,3-isofagomine and alpha- 1,2-mannobiose

Released:
DOI: 10.2210/pdb4utf/pdb
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PDB entry 4utf coloured by chain, front view.
PDB entry 4utf coloured by chain, side view.
PDB entry 4utf coloured by chain, top view.
Source organism: Bacteroides xylanisolvens XB1A
Primary publication:
Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism.
Cuskin F, Lowe EC, Temple MJ, Zhu Y, Cameron E, Pudlo NA, Porter NT, Urs K, Thompson AJ, Cartmell A, Rogowski A, Hamilton BS, Chen R, Tolbert TJ, Piens K, Bracke D, Vervecken W, Hakki Z, Speciale G, Munōz-Munōz JL, Day A, Peña MJ, McLean R, Suits MD, Boraston AB, Atherly T, Ziemer CJ, Williams SJ, Davies GJ, Abbott DW, Martens EC, Gilbert HJ
OpenAccess logo Nature 517 165-169 (2015)
PMID: 25567280

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
Macromolecules (2 distinct):
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
UniProt:
  • Canonical: D6D1V7 (Residues: 1-380; Coverage: 100%)
Gene name: BXY_34140
Sequence domains: Glycosyl hydrolase family 99
Structure domains: Glycosidases

Ligands and Environments

Carbohydrate polymer : NEW Components: MAN
Carbohydrate polymer
3 bound ligands:
Ligand MAN 1 x MAN
Ligand IFM 1 x IFM
Ligand EDO 2 x EDO
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: I4
Unit cell:
a: 108.469Å b: 108.469Å c: 67.755Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.113 0.112 0.139
Expression system: Escherichia coli BL21

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Citations

56 review citations

Introduction to the human gut microbiota.
Thursby et al. (2017)
55 more

1 mention without citation

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism.
Cuskin et al. (2015)

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