1BF2

STRUCTURE OF PSEUDOMONAS ISOAMYLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Three-dimensional structure of Pseudomonas isoamylase at 2.2 A resolution.

Katsuya, Y.Mezaki, Y.Kubota, M.Matsuura, Y.

(1998) J.Mol.Biol. 281: 885-897

  • DOI: 10.1006/jmbi.1998.1992

  • 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 mo ...

    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.


    Organizational Affiliation

    Hyogo Prefectural Institute of Industrial Research, Suma-ku, Kobe, 654-0037, Japan. ykatsuya@hyogo-kp.go.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ISOAMYLASE
A
750Pseudomonas amyloderamosaGene Names: iam
EC: 3.2.1.68
Find proteins for P10342 (Pseudomonas amyloderamosa)
Go to UniProtKB:  P10342
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 138.900α = 90.00
b = 152.400β = 90.00
c = 53.500γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-08-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance