› 8i5q

X-ray diffraction
2.2Å resolution

Crystal structure of TxGH116 D593A acid/base mutant from Thermoanaerobacterium xylanolyticum with laminaribiose

Released:
DOI: 10.2210/pdb8i5q/pdb
PDB entry 8i5q coloured by chain, front view.
PDB entry 8i5q coloured by chain, side view.
PDB entry 8i5q coloured by chain, top view.
Source organism: Thermoanaerobacterium xylanolyticum LX-11
Primary publication:
Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation.
Pengthaisong S, Piniello B, Davies GJ, Rovira C, Ketudat Cairns JR
OpenAccess logo ACS Catal 13 5850-5863 (2023)
PMID: 37180965

Function and Biology Details

Reaction catalysed: 
D-glucosyl-N-acylsphingosine + H(2)O = D-glucose + N-acylsphingosine
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-514549 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Glucosylceramidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 799 amino acids
Theoretical weight: 91.75 KDa
Source organism: Thermoanaerobacterium xylanolyticum LX-11
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: F6BL85 (Residues: 19-806; Coverage: 98%)
Gene name: Thexy_2211
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: BGC
Carbohydrate polymer
3 bound ligands:
Ligand CA 2 x CA
Ligand GOL 1 x GOL
Ligand MES 1 x MES
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL15A1
Spacegroup: P212121
Unit cell:
a: 97.898Å b: 100.625Å c: 173.556Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.191 0.241
Expression system: Escherichia coli BL21(DE3)

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