› 7exu

X-ray diffraction
2.3Å resolution

GH127 beta-L-arabinofuranosidase HypBA1 E322Q mutant complexed with p-nitrophenyl beta-L-arabinofuranoside

Released:
DOI: 10.2210/pdb7exu/pdb
PDB entry 7exu coloured by chain, front view.
PDB entry 7exu coloured by chain, side view.
PDB entry 7exu coloured by chain, top view.
Source organism: Bifidobacterium longum subsp. longum JCM 1217
Primary publication:
Substrate complex structure, active site labeling and catalytic role of the zinc ion in cysteine glycosidase.
Maruyama S, Sawano K, Amaki S, Suzuki T, Narita S, Kimura K, Arakawa T, Yamada C, Ito Y, Dohmae N, Fujita K, Ishiwata A, Fushinobu S
Glycobiology 32 171-180 (2022)
PMID: 34735571

Function and Biology Details

Reaction catalysed: 
Beta-L-arabinofuranosyl-(1->2)-beta-L-arabinofuranose + H(2)O = 2 beta-L-arabinofuranose
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-514046 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Non-reducing end beta-L-arabinofuranosidase Chain: A
Molecule details ›
Chain: A
Length: 669 amino acids
Theoretical weight: 74.46 KDa
Source organism: Bifidobacterium longum subsp. longum JCM 1217
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: E8MGH8 (Residues: 1-658; Coverage: 100%)
Gene names: BLLJ_0211, hypBA1
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand 07Y 1 x 07Y
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P3221
Unit cell:
a: 78.182Å b: 78.182Å c: 253.502Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.254 0.252 0.29
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 citations in other articles

β-l-Arabinofurano-cyclitol Aziridines Are Covalent Broad-Spectrum Inhibitors and Activity-Based Probes for Retaining β-l-Arabinofuranosidases.
Borlandelli et al. (2023)