1Q4N

Structural studies of Phe256Trp of human salivary alpha-amylase: implications for the role of a conserved water molecule and its associated chain in enzyme activity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.159 

Starting Model: experimental
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This is version 2.2 of the entry. See complete history


Literature

Structural studies of a Phe256Trp mutant of human salivary alpha-amylase: implications for the role of a conserved water molecule in enzyme activity

Ramasubbu, N.Sundar, K.Ragunath, C.Rafi, M.M.

(2004) Arch Biochem Biophys 421: 115-124

  • DOI: https://doi.org/10.1016/j.abb.2003.10.007
  • Primary Citation of Related Structures:  
    1Q4N

  • PubMed Abstract: 

    In the mechanism of hydrolysis of starch by alpha-amylases, a conserved water molecule bridging two catalytic residues has been implicated. In human salivary alpha-amylase (HSAmy), this water (W641), observed in many alpha-amylase structures, is part of a chain of water molecules. To test the hypothesis that W641 may be involved in the mechanism, Phe256 in the close vicinity was mutated to a Trp residue. X-ray structure of F256W complexed to 2-amino-2-(hydroxyethyl)-1,3-propanediol at 2.1A revealed that the water chain is disrupted. In the F256W structure exhibits a positional shift in His305, characteristic of alpha-amylase complex structures. Kinetic analysis, in comparison with HSAmy, revealed that the mutant exhibited a 70-fold decrease in the specific activity for starch and significantly reduced k(cat) (20-fold) and K(m) (4-fold) for maltoheptaoside. Collectively, these results suggest that W641 and the chain of water molecules may be critical for the alpha-amylase activity.


  • Organizational Affiliation

    Department of Oral Biology, New Jersey Dental School, University of Medicine and Dentistry, Newark, NJ 07103, USA. n.ramasubbu@umdnj.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-amylase, salivaryA [auth X]496Homo sapiensMutation(s): 1 
Gene Names: AMY1A OR AMY1
EC: 3.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DUB6 (Homo sapiens)
Explore P0DUB6 
Go to UniProtKB:  P0DUB6
GTEx:  ENSG00000237763 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DUB6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A [auth X]L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.9α = 90
b = 74.2β = 90
c = 134.82γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Experimental preparation
  • Version 2.0: 2019-12-25
    Changes: Database references, Derived calculations, Polymer sequence
  • Version 2.1: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 2.2: 2023-08-16
    Changes: Data collection, Refinement description