• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of prosciprotein sciencecshl presssubscriptionsetoc alertsthe protein societyjournal home
Protein Sci. Sep 1995; 4(9): 1730–1742.
PMCID: PMC2143216

The structure of human pancreatic alpha-amylase at 1.8 A resolution and comparisons with related enzymes.


The structure of human pancreatic alpha-amylase has been determined to 1.8 A resolution using X-ray diffraction techniques. This enzyme is found to be composed of three structural domains. The largest is Domain A (residues 1-99, 169-404), which forms a central eight-stranded parallel beta-barrel, to one end of which are located the active site residues Asp 197, Glu 233, and Asp 300. Also found in this vicinity is a bound chloride ion that forms ligand interactions to Arg 195, Asn 298, and Arg 337. Domain B is the smallest (residues 100-168) and serves to form a calcium binding site against the wall of the beta-barrel of Domain A. Protein groups making ligand interactions to this calcium include Asn 100, Arg 158, Asp 167, and His 201. Domain C (residues 405-496) is made up of anti-parallel beta-structure and is only loosely associated with Domains A and B. It is notable that the N-terminal glutamine residue of human pancreatic alpha-amylase undergoes a posttranslational modification to form a stable pyrrolidone derivative that may provide protection against other digestive enzymes. Structure-based comparisons of human pancreatic alpha-amylase with functionally related enzymes serve to emphasize three points. Firstly, despite this approach facilitating primary sequence alignments with respect to the numerous insertions and deletions present, overall there is only approximately 15% sequence homology between the mammalian and fungal alpha-amylases. Secondly, in contrast, these same studies indicate that significant structural homology is present and of the order of approximately 70%. Thirdly, the positioning of Domain C can vary considerably between alpha-amylases. In terms of the more closely related porcine enzyme, there are four regions of polypeptide chain (residues 237-250, 304-310, 346-354, and 458-461) with significantly different conformations from those in human pancreatic alpha-amylase. At least two of these could play a role in observed differential substrate and cleavage pattern specificities between these enzymes. Similarly, amino acid differences between human pancreatic and salivary alpha-amylases have been localized and a number of these occur in the vicinity of the active site.

Full Text

The Full Text of this article is available as a PDF (2.3M).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. [PubMed]
  • Boel E, Brady L, Brzozowski AM, Derewenda Z, Dodson GG, Jensen VJ, Petersen SB, Swift H, Thim L, Woldike HF. Calcium binding in alpha-amylases: an X-ray diffraction study at 2.1-A resolution of two enzymes from Aspergillus. Biochemistry. 1990 Jul 3;29(26):6244–6249. [PubMed]
  • Brady RL, Brzozowski AM, Derewenda ZS, Dodson EJ, Dodson GG. Solution of the structure of Aspergillus niger acid alpha-amylase by combined molecular replacement and multiple isomorphous replacement methods. Acta Crystallogr B. 1991 Aug 1;47(Pt 4):527–535. [PubMed]
  • Brogard JM, Willemin B, Blicklé JF, Lamalle AM, Stahl A. Inhibiteurs des alpha-glucosidases: une nouvelle approche thérapeutique du diabète et des hypoglycémies fonctionnelles. Rev Med Interne. 1989 Jul-Aug;10(4):365–374. [PubMed]
  • Burk D, Wang Y, Dombroski D, Berghuis AM, Evans SV, Luo Y, Withers SG, Brayer GD. Isolation, crystallization and preliminary diffraction analyses of human pancreatic alpha-amylase. J Mol Biol. 1993 Apr 5;230(3):1084–1085. [PubMed]
  • Gumucio DL, Wiebauer K, Caldwell RM, Samuelson LC, Meisler MH. Concerted evolution of human amylase genes. Mol Cell Biol. 1988 Mar;8(3):1197–1205. [PMC free article] [PubMed]
  • Hendrickson WA. Stereochemically restrained refinement of macromolecular structures. Methods Enzymol. 1985;115:252–270. [PubMed]
  • Jespersen HM, MacGregor EA, Henrissat B, Sierks MR, Svensson B. Starch- and glycogen-debranching and branching enzymes: prediction of structural features of the catalytic (beta/alpha)8-barrel domain and evolutionary relationship to other amylolytic enzymes. J Protein Chem. 1993 Dec;12(6):791–805. [PubMed]
  • Kadziola A, Abe J, Svensson B, Haser R. Crystal and molecular structure of barley alpha-amylase. J Mol Biol. 1994 May 27;239(1):104–121. [PubMed]
  • Kluh I. Amino acid sequence of hog pancreatic alpha-amylase isoenzyme I. FEBS Lett. 1981 Dec 28;136(2):231–234. [PubMed]
  • Larson SB, Greenwood A, Cascio D, Day J, McPherson A. Refined molecular structure of pig pancreatic alpha-amylase at 2.1 A resolution. J Mol Biol. 1994 Feb 4;235(5):1560–1584. [PubMed]
  • Levitzki A, Steer ML. The allosteric activation of mammalian alpha-amylase by chloride. Eur J Biochem. 1974 Jan 3;41(1):171–180. [PubMed]
  • Lifshitz R, Levitzki A. Identity and properties of the chloride effector binding site in hog pancreatic alpha-amylase. Biochemistry. 1976 May 4;15(9):1987–1993. [PubMed]
  • LOYTER A, SCHRAMM M. The glycogen-amylase complex as a means of obtaining highly purified alpha-amylases. Biochim Biophys Acta. 1962 Dec 4;65:200–206. [PubMed]
  • MacGregor EA. Alpha-amylase structure and activity. J Protein Chem. 1988 Aug;7(4):399–415. [PubMed]
  • Nishide T, Emi M, Nakamura Y, Matsubara K. Corrected sequences of cDNAs for human salivary and pancreatic alpha-amylases [corrected]. Gene. 1984 May;28(2):263–270. [PubMed]
  • Pasero L, Mazzéi-Pierron Y, Abadie B, Chicheportiche Y, Marchis-Mouren G. Complete amino acid sequence and location of the five disulfide bridges in porcine pancreatic alpha-amylase. Biochim Biophys Acta. 1986 Jan 30;869(2):147–157. [PubMed]
  • Qian M, Haser R, Buisson G, Duée E, Payan F. The active center of a mammalian alpha-amylase. Structure of the complex of a pancreatic alpha-amylase with a carbohydrate inhibitor refined to 2.2-A resolution. Biochemistry. 1994 May 24;33(20):6284–6294. [PubMed]
  • Qian M, Haser R, Payan F. Structure and molecular model refinement of pig pancreatic alpha-amylase at 2.1 A resolution. J Mol Biol. 1993 Jun 5;231(3):785–799. [PubMed]
  • Svens E, Käpyaho K, Tanner P, Weber TH. Immunocatalytic assay of pancreatic alpha-amylase in serum and urine with a specific monoclonal antibody. Clin Chem. 1989 Apr;35(4):662–664. [PubMed]
  • Swift HJ, Brady L, Derewenda ZS, Dodson EJ, Dodson GG, Turkenburg JP, Wilkinson AJ. Structure and molecular model refinement of Aspergillus oryzae (TAKA) alpha-amylase: an application of the simulated-annealing method. Acta Crystallogr B. 1991 Aug 1;47(Pt 4):535–544. [PubMed]
  • Takkinen K, Pettersson RF, Kalkkinen N, Palva I, Söderlund H, Käriäinen L. Amino acid sequence of alpha-amylase from Bacillus amyloliquefaciens deduced from the nucleotide sequence of the cloned gene. J Biol Chem. 1983 Jan 25;258(2):1007–1013. [PubMed]
  • VALLEE BL, STEIN EA, SUMERWELL WN, FISCHER EH. Metal content of alpha-amylases of various origins. J Biol Chem. 1959 Nov;234:2901–2905. [PubMed]
  • Wise RJ, Karn RC, Larsen SH, Hodes ME, Gardell SJ, Rutter WJ. A complementary DNA sequence that predicts a human pancreatic amylase primary structure consistent with the electrophoretic mobility of the common isozyme, Amy2 A. Mol Biol Med. 1984 Oct;2(5):307–322. [PubMed]

Articles from Protein Science : A Publication of the Protein Society are provided here courtesy of The Protein Society


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...