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(-) Description

Title :  THE CRYSTAL STRUCTURE AND PROPOSED AMINO ACID SEQUENCE OF A PEPSIN FROM ATLANTIC COD (GADUS MORHUA)
 
Authors :  S. Karlsen, E. Hough, R. L. Olsen
Date :  23 Jun 97  (Deposition) - 24 Dec 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym./Biol. Unit :  A
Keywords :  Aspartyl Protease, Acid Proteinase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Karlsen, E. Hough, R. L. Olsen
Structure And Proposed Amino-Acid Sequence Of A Pepsin From Atlantic Cod (Gadus Morhua).
Acta Crystallogr. , Sect. D V. 54 32 1998
PubMed-ID: 9761815  |  Reference-DOI: 10.1107/S090744499700810X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPSIN
    Chains: A
    EC Number: 3.4.23.1
    Organ: STOMACH
    Organism Common: ATLANTIC COD
    Organism Scientific: GADUS MORHUA
    Organism Taxid: 8049
    Synonym: ACID PROTEINASE
    Tissue: GASTRIC MUCOSA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1AM5)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1CATUNKNOWNASP A:32 , ASP A:215THE CATALYTIC ASPARTIC RESIDUES, ASP 32 AND ASP 215, ARE CONNECTED THROUGH A NETWORK OF HYDROGEN BONDS.

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:45 -A:50
2A:206 -A:210
3A:249 -A:282

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:22 -Pro A:23

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AM5)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.PEP2B_GADMO14-321  1A:14-323
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.PEP2B_GADMO29-40
211-222		  2A:29-40
A:212-223

(-) Exons   (0, 0)

(no "Exon" information available for 1AM5)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:324
 aligned with PEP2B_GADMO | P56272 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:324
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320    
          PEP2B_GADMO     1 RVTEQMKNEADTEYYGVISIGTPPESFKVIFDTGSSNLWVSSSHCSAQACSNHNKFKPRQSSTYVETGKTVDLTYGTGGMRGILGQDTVSVGGGSDPNQELGESQTEPGPFQAAAPFDGILGLAYPSIAAAGAVPVFDNMGSQSLVEKDLFSFYLSGGGANGSEVMLGGVDNSHYTGSIHWIPVTAEKYWQVALDGITVNGQTAACEGCQAIVDTGTSKIVAPVSALANIMKDIGASENQGEMMGNCASVQSLPDITFTINGVKQPLPPSAYIEGDQAFCTSGLGSSGVPSNTSELWIFGDVFLRNYYTIYDRTNNKVGFAPAA 324
               SCOP domains d1am5a_ A: Pepsin(ogen)                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1am5A01 A:1-170 Acid Proteases                                                                                                                                            1am5A02 A:171-324 Acid Proteases                                                                                                                        -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee...eeeeeeee....eeeeeeee.....eee.......hhhhh.....hhh.........eeeee....eeeeeeeee...........eeeeeeee............eeee...hhh.hhh...hhhhhhh.......eeeee........eeeee....hhh.....eeee.......eeee.eeee.........eeeee......eee...hhhhhhhhh.....................eeeee..eeeee.hhhheee....eee.eee.........eeee.hhhhhheeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -------------PEPTIDASE_A1  PDB: A:14-323 UniProt: 14-321                                                                                                                                                                                                                                                                         --- PROSITE (1)
                PROSITE (2) ----------------------------ASP_PROTEASE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1am5 A   1 RVTEQMKNEADTEYYGVISIGTPPESFKVIFDTGSSNLWVSSSHCSAQACSNHNKFKPRQSSTYVETGKTVDLTYGTGGMRGILGQDTVSVGGGSDPNQELGESQTEPGPFQAAAPFDGILGLAYPSIAAAGAVPVFDNMGSQSLVEKDLFSFYLSGGGANGSEVMLGGVDNSHYTGSIHWIPVTAEKYWQVALDGITVNGQTAACEGCQAIVDTGTSKIVAPVSALANIMKDIGASENQGEMMGNCASVQSLPDITFTINGVKQPLPPSAYIEGDQAFCTSGLGSSGVPSNTSELWIFGDVFLRNYYTIYDRTNNKVGFAPAA 326
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     ||211       221       231       242       252       262       272       282       292       302       312       322    
                                                                                                                                                                                                                                       206|                             240|                                                                                    
                                                                                                                                                                                                                                        208                              242
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AM5)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PEP2B_GADMO | P56272)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0007586    digestion    The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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