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PDBsum entry 1smd

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Hydrolase (o-glycosyl) PDB id
1smd
Jmol
Contents
Protein chain
496 a.a.
Metals
_CL
_CA
Waters ×169

References listed in PDB file
Key reference
Title Structure of human salivary alpha-Amylase at 1.6 a resolution: implications for its role in the oral cavity.
Authors N.Ramasubbu, V.Paloth, Y.Luo, G.D.Brayer, M.J.Levine.
Ref. Acta Crystallogr D Biol Crystallogr, 1996, 52, 435-446. [DOI no: 10.1107/S0907444995014119]
PubMed id 15299664
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 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.
Figure 7.
Fig. 7. Influence of two salt bridges on the regularity of helix composed of residues 20-33. The first such interation between Glu27 and Arg30 breaks the helix at Tyr31. The second, the result of interaction between Arg20 and Asp23, creates a bulge near the N-terminus of this helical segment.
Figure 9.
Fig. 9. The conformation of a potential N-glycosylation site in saliary amylase. Ser414 at the center f the site is influenced by intraolec- ular interactions with Asn412 and Asp432 This conformation observed is ignificantly different from that adopted by synthetic peptides that gt glycosylated (Pinchion-Pesme et al., 1988).
The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1996, 52, 435-446) copyright 1996.
Secondary reference #1
Title Crystallization and preliminary X-Ray diffraction analysis of human salivary alpha-Amylase
Authors N.Ramasubbu, K.K.Bhandary, F.A.Scannapieco, M.J.Levine.
Ref. proteins: struct.,funct.,, 1991, 11, 230.
Secondary reference #2
Title Structural relationship between the enzymatic and streptococcal binding sites of human salivary alpha-Amylase.
Authors F.A.Scannapieco, K.Bhandary, N.Ramasubbu, M.J.Levine.
Ref. Biochem Biophys Res Commun, 1990, 173, 1109-1115.
PubMed id 2125215
Abstract
PROCHECK
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