1NM9

Crystal structure of recombinant human salivary amylase mutant W58A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 3.2 of the entry. See complete history


Literature

Human salivary alpha-amylase Trp58 situated at subsite -2 is critical for enzyme activity.

Ramasubbu, N.Ragunath, C.Mishra, P.J.Thomas, L.M.Kandra, L.

(2004) Eur J Biochem 271: 2517-2529

  • DOI: https://doi.org/10.1111/j.1432-1033.2004.04182.x
  • Primary Citation of Related Structures:  
    1JXJ, 1NM9

  • PubMed Abstract: 

    The nonreducing end of the substrate-binding site of human salivary alpha-amylase contains two residues Trp58 and Trp59, which belong to beta2-alpha2 loop of the catalytic (beta/alpha)(8) barrel. While Trp59 stacks onto the substrate, the exact role of Trp58 is unknown. To investigate its role in enzyme activity the residue Trp58 was mutated to Ala, Leu or Tyr. Kinetic analysis of the wild-type and mutant enzymes was carried out with starch and oligosaccharides as substrates. All three mutants exhibited a reduction in specific activity (150-180-fold lower than the wild type) with starch as substrate. With oligosaccharides as substrates, a reduction in k(cat), an increase in K(m) and distinct differences in the cleavage pattern were observed for the mutants W58A and W58L compared with the wild type. Glucose was the smallest product generated by these two mutants in the hydrolysis oligosaccharides; in contrast, wild-type enzyme generated maltose as the smallest product. The production of glucose by W58L was confirmed from both reducing and nonreducing ends of CNP-labeled oligosaccharide substrates. The mutant W58L exhibited lower binding affinity at subsites -2, -3 and +2 and showed an increase in transglycosylation activity compared with the wild type. The lowered affinity at subsites -2 and -3 due to the mutation was also inferred from the electron density at these subsites in the structure of W58A in complex with acarbose-derived pseudooligosaccharide. Collectively, these results suggest that the residue Trp58 plays a critical role in substrate binding and hydrolytic activity of human salivary alpha-amylase.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-amylase, salivary496Homo sapiensMutation(s): 1 
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
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
4-amino-4,6-dideoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B, C
2N/A
Glycosylation Resources
GlyTouCan:  G90989WB
GlyCosmos:  G90989WB
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.946α = 90
b = 74.06β = 90
c = 134.508γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-20
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-12-25
    Changes: Advisory, Data collection, Database references, Derived calculations, Polymer sequence
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2021-10-27
    Changes: Database references, Derived calculations, Structure summary
  • Version 3.2: 2023-08-16
    Changes: Data collection, Refinement description