› 4amw

X-ray diffraction
1.9Å resolution

CRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- GLUCAN LYASE Covalent Intermediate Complex with 5-fluoro-idosyl- fluoride

Released:
DOI: 10.2210/pdb4amw/pdb
PDB entry 4amw coloured by chain, front view.
PDB entry 4amw coloured by chain, side view.
PDB entry 4amw coloured by chain, top view.
Source organism: Gracilariopsis lemaneiformis
Primary publication:
Crystal structure of α-1,4-glucan lyase, a unique glycoside hydrolase family member with a novel catalytic mechanism.
Rozeboom HJ, Yu S, Madrid S, Kalk KH, Zhang R, Dijkstra BW
J Biol Chem 288 26764-74 (2013)
PMID: 23902768

Function and Biology Details

Reaction catalysed: 
Linear alpha-glucan = (n-1) 1,5-anhydro-D-fructose + D-glucose
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193531 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glucosidase II subunit alpha Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 1027 amino acids
Theoretical weight: 116.06 KDa
Source organism: Gracilariopsis lemaneiformis
Expression system: Ogataea polymorpha RB11
UniProt:
  • Canonical: Q9STC1 (Residues: 62-1088; Coverage: 94%)
Gene name: Ag111
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand B9D 3 x B9D
Ligand GOL 7 x GOL
Ligand 5DI 1 x 5DI
1 modified residue:
Ligand CSO 4 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P1
Unit cell:
a: 92.1Å b: 97.3Å c: 136.28Å
α: 80.31° β: 83.29° γ: 85.21°
R-values:
R R work R free
0.209 0.207 0.254
Expression system: Ogataea polymorpha RB11

Quick links

Citations

2 review citations

α-Glucosidases and α-1,4-glucan lyases: structures, functions, and physiological actions.
Okuyama et al. (2016)
1 more

2 mentions without citation

Self-association of a highly charged arginine-rich cell-penetrating peptide.
Tesei et al. (2017)
1 more