1AM5

THE CRYSTAL STRUCTURE AND PROPOSED AMINO ACID SEQUENCE OF A PEPSIN FROM ATLANTIC COD (GADUS MORHUA)

Summary for 1AM5

• Entry DOI: 10.2210/pdb1am5/pdb
• Descriptor: PEPSIN (2 entities in total)
• Functional Keywords: aspartyl protease, acid proteinase, hydrolase
• Biological source: Gadus morhua (Atlantic cod)
• Total number of polymer chains: 1
• Total formula weight: 34033.56

Authors

Karlsen, S.,Hough, E.,Olsen, R.L. (deposition date: 1997-06-23, release date: 1997-12-24, Last modification date: 2023-08-02)

Primary citation

Karlsen, S.,Hough, E.,Olsen, R.L.
Structure and proposed amino-acid sequence of a pepsin from atlantic cod (Gadus morhua).
Acta Crystallogr.,Sect.D, 54:32-46, 1998

PubMed Abstract: The crystal structure of a pepsin from the gastric mucosa of Atlantic cod has been determined to 2.16 A resolution. Data were collected on orthorhombic crystals with cell dimensions a = 35.98, b = 75.40 and c = 108.10 A, on a FAST area-detector system. The phase problem was solved by the molecular-replacement method using porcine pepsin (PDB entry 5PEP) as a search model. The structure has been refined to a crystallographic R factor of 20.8% using all reflections between 8.0 and 2.16 A, without prior knowledge of the primary sequence. The resulting crystal structure is very similar to the porcine enzyme, consisting of two domains with predominantly beta-sheet structure in the same sequential positions as the enzyme from pig. In the course of the model building, 122 residues were substituted and two residues deleted from the starting model to give a polypeptide chain of 324 amino acids and a sequence identity of 57.7% with the pig pepsin. No carbohydrate residues were located. Sequence alignment with available aspartic proteinases, indicates that the fish enzyme seems to be more related to mammalian gastric pepsins than to the mammalian gastricsins and chymosins, lysosomal cathepsin D's and a pepsin from tuna fish. The amino-acid composition of the cod enzyme, however, is more in accordance with the cathepsin D's.

PubMed: 9761815
DOI: 10.1107/S090744499700810X

Experimental method

X-RAY DIFFRACTION (2.16 Å)