CRYSTAL STRUCTURE OF HUMAN PEPSINOGEN A. Katherine S. Bateman1, Maia N. Chernaia1, Nadya I. Tarasova2, Michael N. G. James1, 1MRC Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada TOG 2H7, 2Molecular Aspects of Drug Design Section, ABL-Basic Research Program, National Cancer Institute, FCDRC, P. O. Box B, Frederick, Maryland 21702
The three dimensional structure of human pepsinogen A has been solved by the method of molecular replacement. The protein fold is similar to those of previously determined aspartic proteinase zymogens, porcine pepsinogen[1] and human progastricsin[2]. Two similar domains consisting mostly of [[beta]]-sheet make up the enzymatic portion of the zymogen. A smaller segment of two [[beta]]-strands and short [[alpha]]-helices sits between the two large domains in the active site cleft.
Pepsinogen is the inactive protein precursor of pepsin, an aspartic proteinase found in the gastric mucosa. A 46 amino acid prosegment is removed by autocleavage once pepsinogen has been exposed to acidic pH. Before enzyme activation, a portion of the prosegment occupies and blocks the binding cleft. The catalytic aspartic acid residues 32 and 215 are electostatically stabilized by residues Lys36p, Tyr37p and Tyr9, p denoting residues of the prosegment. A conformational rearrangement accompanies a pH decrease which then allows access to the binding site. Aspartic proteinases are critical in many metabolic pathways such as the regulation of blood pressure. Regulation of aspartic proteinases through drug design will be greatly assisted by an understanding of biological mechanisms for enzyme inhibition and control.
Crystals of human pepsinogen A were grown in space group P21212 having unit cell dimensions a=91.6, b=105.2, c=40.2 Å with one molecule per asymmetric unit. High resolution data were collected at the Photon Factory in Tsukuba, Japan to 1.7 Å. The program AMORE[3] was used to solve the structure by molecular replacement with porcine pepsinogen A[1] as the replacement model. The model is currently being refined; the R-factor and R-free of the present model being 21.6% and 29.7% respectively from 20 to 2 Å.
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