1am5
From Proteopedia
| Line 5: | Line 5: | ||
==Overview== | ==Overview== | ||
| - | 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 ... | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1AM5 is a | + | 1AM5 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Gadus_morhua Gadus morhua]. Active as [http://en.wikipedia.org/wiki/Pepsin_A Pepsin A], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.1 3.4.23.1] Structure known Active Site: CAT. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1AM5 OCA]. |
==Reference== | ==Reference== | ||
| Line 22: | Line 22: | ||
[[Category: hydrolase]] | [[Category: hydrolase]] | ||
| - | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 13:34:33 2007'' |
Revision as of 11:29, 5 November 2007
|
THE CRYSTAL STRUCTURE AND PROPOSED AMINO ACID SEQUENCE OF A PEPSIN FROM ATLANTIC COD (GADUS MORHUA)
Overview
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.
About this Structure
1AM5 is a Single protein structure of sequence from Gadus morhua. Active as Pepsin A, with EC number 3.4.23.1 Structure known Active Site: CAT. Full crystallographic information is available from OCA.
Reference
Structure and proposed amino-acid sequence of a pepsin from atlantic cod (Gadus morhua)., Karlsen S, Hough E, Olsen RL, Acta Crystallogr D Biol Crystallogr. 1998 Jan 1;54(Pt 1):32-46. PMID:9761815
Page seeded by OCA on Mon Nov 5 13:34:33 2007
