spacer
spacer

PDBsum entry 1dog

Go to PDB code: 
Top Page protein ligands links
Hydrolase PDB id
1dog
Jmol
Contents
Protein chain
470 a.a.
Ligands
NAG-NAG-BMA-MAN-
MAN
NAG-NAG-BMA-MAN-
MAN-MAN-MAN-MAN
MAN ×10
NOJ ×2
Waters ×605

References listed in PDB file
Key reference
Title Refined structure for the complex of 1-Deoxynojirimycin with glucoamylase from aspergillus awamori var. X100 to 2.4-A resolution.
Authors E.M.Harris, A.E.Aleshin, L.M.Firsov, R.B.Honzatko.
Ref. Biochemistry, 1993, 32, 1618-1626. [DOI no: 10.1021/bi00057a028]
PubMed id 8431441
Abstract
The three-dimensional structure of the complex of 1-deoxynojirimycin with glucoamylase II-(471) from Aspergillus awamori var. X100 has been determined to 2.4-A resolution. The model includes residues corresponding to residues 1-471 of glucoamylase I from Aspergillus niger, two molecules of bound 1-deoxynojirimycin and 605 sites for water molecules. The crystallographic R factor from refinement is 0.119, and the root-mean-squared deviation in bond distances is 0.012 A. The inhibitor complex confirms the location of the active site in the packing void of the alpha/alpha-barrel as proposed by Aleshin et al. [Aleshin, A., Golubev, A., Firsov, L., & Honzatko, R. B. (1992) J. Biol. Chem. 267, 19291-19298]. One inhibitor molecule is associated with strong electron density and represents the principal site of interaction of 1-deoxynojirimycin with the enzyme. The other 1-deoxynojirimycin molecule is associated with weak electron density and therefore, probably represents a binding site of low affinity. Interactions of 1-deoxynojirimycin with the enzyme at its principal site involve Arg 45, Asp 55, Arg 305, and carbonyl 177. In addition, a water molecule (water 500) hydrogen bonds to Glu 400 and the 6-hydroxyl of 1-deoxynojirimycin and is at an approximate distance of 3.3 A from the "anomeric" carbon of the inhibitor. The structural arrangement of functional groups near the inhibitor molecule suggests that Glu 179 is a catalytic acid, Glu 400 a catalytic base, and water 500 the attacking nucleophile in the hydrolysis of maltooligosaccharides. The relevance of the X-ray work to proposed mechanisms of enzymatic hydrolysis of oligosaccharides is discussed.
Secondary reference #1
Title Crystal structure of glucoamylase from aspergillus awamori var. X100 to 2.2-A resolution.
Authors A.Aleshin, A.Golubev, L.M.Firsov, R.B.Honzatko.
Ref. J Biol Chem, 1992, 267, 19291-19298.
PubMed id 1527049
Abstract
PROCHECK
Go to PROCHECK summary
 Headers