1SMD

HUMAN SALIVARY AMYLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of human salivary alpha-amylase at 1.6 A resolution: implications for its role in the oral cavity.

Ramasubbu, N.Paloth, V.Luo, Y.Brayer, G.D.Levine, M.J.

(1996) Acta Crystallogr.,Sect.D 52: 435-446

  • DOI: 10.1107/S0907444995014119

  • PubMed Abstract: 
  • Salivary alpha-amylase, a major component of human saliva, plays a role in the initial digestion of starch and may be involved in the colonization of bacteria involved in early dental plaque formation. The three-dimensional atomic structure of saliva ...

    Salivary alpha-amylase, a major component of human saliva, plays a role in the initial digestion of starch and may be involved in the colonization of bacteria involved in early dental plaque formation. The three-dimensional atomic structure of salivary amylase has been determined to understand the structure-function relationships of this enzyme. This structure was refined to an R value of 18.4% with 496 amino-acid residues, one calcium ion, one chloride ion and 170 water molecules. Salivary amylase folds into a multidomain structure consisting of three domains, A, B and C. Domain A has a (beta/alpha)(8-) barrel structure, domain B has no definite topology and domain C has a Greek-key barrel structure. The Ca(2+) ion is bound to Asnl00, Arg158, Asp167, His201 and three water molecules. The Cl(-) ion is bound to Arg195, Asn298 and Arg337 and one water molecule. The highly mobile glycine-rich loop 304-310 may act as a gateway for substrate binding and be involved in a 'trap-release' mechanism in the hydrolysis of substrates. Strategic placement of calcium and chloride ions, as well as histidine and tryptophan residues may play a role in differentiating between the glycone and aglycone ends of the polysaccharide substrates. Salivary amylase also possesses a suitable site for binding to enamel surfaces and provides potential sites for the binding of bacterial adhesins.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Diffraction Analysis of Human Salivary Alpha-Amylase
      Ramasubbu, N.,Bhandary, K.K.,Scannapieco, F.A.,Levine, M.J.
      (1991) Proteins 11: 230
    • Structural Relationship between the Enzymatic and Streptococcal Binding Sites of Human Salivary Alpha-Amylase
      Scannapieco, F.A.,Bhandary, K.,Ramasubbu, N.,Levine, M.J.
      (1990) Biochem.Biophys.Res.Commun. 173: 1109


    Organizational Affiliation

    Department of Oral Biology and Dental Research Institute, School of Dental Medicine, State University of New York at Buffalo, BY 14214, USA. subbu@crystal1.sdm.buffalo.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AMYLASE
A
496Homo sapiensGene Names: AMY1A, AMY1B, AMY1C (AMY1, AMY1, AMY1)
EC: 3.2.1.1
Find proteins for P04745 (Homo sapiens)
Go to Gene View: AMY1A AMY1B AMY1C
Go to UniProtKB:  P04745
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.200α = 90.00
b = 75.400β = 90.00
c = 136.600γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1996-01-24 
  • Released Date: 1996-07-11 
  • Deposition Author(s): Ramasubbu, N.

Revision History 

  • Version 1.0: 1996-07-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance