1AM5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.208 

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This is version 1.3 of the entry. See complete history


Literature

Structure and proposed amino-acid sequence of a pepsin from atlantic cod (Gadus morhua).

Karlsen, S.Hough, E.Olsen, R.L.

(1998) Acta Crystallogr D Biol Crystallogr 54: 32-46

  • DOI: 10.1107/s090744499700810x
  • Primary Citation of Related Structures:  
    1AM5

  • 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 syste ...

    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.


    Related Citations: 
    • Catalytic Properties and Chemical Composition of Pepsins from Atlantic Cod (Gadus Morhua)
      Gildberg, A., Olsen, R.L., Bjarnason, J.B.
      (1990) Comp Biochem Physiol B 96: 323

    Organizational Affiliation

    Protein Crystallography Group, Department of Chemistry, Faculty of Science, University of Tromso, N-9037 Tromso, Norway.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEPSINA324Gadus morhuaMutation(s): 0 
EC: 3.4.23.1 (PDB Primary Data), 3.4.23 (UniProt)
Find proteins for P56272 (Gadus morhua)
Explore P56272 
Go to UniProtKB:  P56272
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.16 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.98α = 90
b = 75.4β = 90
c = 108.1γ = 90
Software Package:
Software NamePurpose
MADNESdata collection
CCP4data reduction
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
MADNESdata reduction
CCP4data scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-12-24
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-18
    Changes: Data collection, Other