1BF2

STRUCTURE OF PSEUDOMONAS ISOAMYLASE

Summary for 1BF2

• Entry DOI: 10.2210/pdb1bf2/pdb
• Descriptor: ISOAMYLASE, CALCIUM ION (3 entities in total)
• Functional Keywords: hydrolase, glycosidase, debranching enzyme
• Biological source: Pseudomonas amyloderamosa
• Total number of polymer chains: 1
• Total formula weight: 81180.06

Authors

Katsuya, Y.,Mezaki, Y.,Kubota, M.,Matsuura, Y. (deposition date: 1998-05-26, release date: 1998-08-12, Last modification date: 2024-10-23)

Primary citation

Katsuya, Y.,Mezaki, Y.,Kubota, M.,Matsuura, Y.
Three-dimensional structure of Pseudomonas isoamylase at 2.2 A resolution.
J.Mol.Biol., 281:885-897, 1998

PubMed Abstract: The three-dimensional structure of isoamylase from Pseudomonas amyloderamosa, which hydrolyzes alpha-1,6-glucosidic linkages of amylopectin and glycogen, has been determined by X-ray structure analysis. The enzyme has 750 amino acid residues and a molecular mass of 80 kDa, and it can be crystallized from ammonium sulfate solution. The structure was elucidated by the multiple isomorphous replacement method and refined at 2.2 A resolution, resulting in a final R-factor of 0.161 for significant reflections with a root-mean-square deviation from ideality in bond lengths of 0.009 A. The analysis revealed that in the N-terminal region, isoamylase has a novel extra domain that we call domain N, whose three-dimensional structure has not so far been reported. It has a (beta/alpha)8-barrel-type supersecondary structure in the catalytic domain common to the alpha-amylase family enzymes, though the barrel is incomplete, with a deletion of an alpha-helix between the fifth and sixth beta-strands. A long excursed region is present between the third beta-strand and the third alpha-helix of the barrel but, in contrast to the so-called domain B that has been identified in the other enzymes of alpha-amylase family, it cannot be considered to be an independent domain, because this loop forms a globular cluster together with the loop between the fourth beta-strand and the fourth alpha-helix. Isoamylase contains a bound calcium ion, but this is not in the same position as the conserved calcium ion that has been reported in other alpha-amylase family enzymes.

PubMed: 9719642
DOI: 10.1006/jmbi.1998.1992

Experimental method

X-RAY DIFFRACTION (2 Å)