1QPK

MUTANT (D193G) MALTOTETRAOSE-FORMING EXO-AMYLASE IN COMPLEX WITH MALTOTETRAOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report



Literature

Roles of catalytic residues in alpha-amylases as evidenced by the structures of the product-complexed mutants of a maltotetraose-forming amylase.

Hasegawa, K.Kubota, M.Matsuura, Y.

(1999) Protein Eng 12: 819-824

  • DOI: 10.1093/protein/12.10.819
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structures of the four product-complexed single mutants of the catalytic residues of Pseudomonas stutzeri maltotetraose-forming alpha-amylase, E219G, D193N, D193G and D294N, have been determined. Possible roles of the catalytic residues G ...

    The crystal structures of the four product-complexed single mutants of the catalytic residues of Pseudomonas stutzeri maltotetraose-forming alpha-amylase, E219G, D193N, D193G and D294N, have been determined. Possible roles of the catalytic residues Glu219, Asp193 and Asp294 have been discussed by comparing the structures among the previously determined complexed mutant E219Q and the present mutant enzymes. The results suggested that Asp193 predominantly works as the base catalyst (nucleophile), whose side chain atom lies in close proximity to the C1-atom of Glc4, being involved in the intermediate formation in the hydrolysis reaction. While Asp294 works for tightly binding the substrate to give a twisted and a deformed conformation of the glucose ring at position -1 (Glc4). The hydrogen bond between the side chain atom of Glu219 and the O1-atom of Glc4, that implies the possibility of interaction via hydrogen, consistently present throughout these analyses, supports the generally accepted role of this residue as the acid catalyst (proton donor).


    Related Citations: 
    • Crystal Structures of a Mutant Maltotetraose-Forming Exo-Amylase Cocrystallized with Maltopentaose
      Yoshioka, Y., Hasegawa, K., Matsuura, Y., Katsube, Y., Kubota, M.
      (1997) J Mol Biol 271: 619
    • Crystal Structure of a Maltotetraose-Forming Exo-Amylase from Pseudomonas Stutzeri
      Morishita, Y., Hasegawa, K., Matsuura, Y., Katsube, Y., Kubota, M.
      (1997) J Mol Biol 267: 661

    Organizational Affiliation

    Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (MALTOTETRAOSE-FORMING AMYLASE)A418Pseudomonas stutzeriMutation(s): 1 
Gene Names: amyP
EC: 3.2.1.60
Find proteins for P13507 (Pseudomonas stutzeri)
Explore P13507 
Go to UniProtKB:  P13507
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Oligosaccharides
Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
4 N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.21α = 90
b = 167.5β = 90
c = 46.72γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PROFFTrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-11-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary