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(-) Description

Title :  EFFECT OF DIMETHYL SULPHOXIDE ON THE CRYSTAL STRUCTURE OF PORCINE PEPSIN
 
Authors :  M. M. Kesavulu, S. Ramasubramanian, K. Suguna
Date :  20 Feb 05  (Deposition) - 24 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Pepsin, Dimethyl Sulphoxide, Protein Denaturation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Kesavulu, S. Ramasubramanian, K. Suguna
Effect Of Dimethyl Sulphoxide On The Crystal Structure Of Porcine Pepsin.
Biochem. Biophys. Res. Commun. V. 331 1510 2005
PubMed-ID: 15883044  |  Reference-DOI: 10.1016/J.BBRC.2005.03.247
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPSINOGEN A
    Chains: A
    EC Number: 3.4.23.1
    Fragment: PEPSIN
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:53 , ASN A:54 , GLN A:55 , SER A:172BINDING SITE FOR RESIDUE DMS A 500

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:45 -A:50
2A:206 -A:210
3A:250 -A:283

(-) 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 1YX9)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.PEPA_PIG73-382  1A:14-324
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.PEPA_PIG88-99
271-282		  2A:29-40
A:212-223

(-) Exons   (0, 0)

(no "Exon" information available for 1YX9)

(-) 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:326
 aligned with PEPA_PIG | P00791 from UniProtKB/Swiss-Prot  Length:385

    Alignment length:326
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379      
             PEPA_PIG    60 IGDEPLENYLDTEYFGTIGIGTPAQDFTVIFDTGSSNLWVPSVYCSSLACSDHNQFNPDDSSTFEATSQELSITYGTGSMTGILGYDTVQVGGISDTNQIFGLSETEPGSFLYYAPFDGILGLAYPSISASGATPVFDNLWDQGLVSQDLFSVYLSSNDDSGSVVLLGGIDSSYYTGSLNWVPVSVEGYWQITLDSITMDGETIACSGGCQAIVDTGTSLLTGPTSAIANIQSDIGASENSDGEMVISCSSIDSLPDIVFTINGVQYPLSPSAYILQDDDSCTSGFEGMDVPTSSGELWILGDVFIRQYYTVFDRANNKVGLAPVA 385
               SCOP domains d1yx9a_ A: Pepsin(ogen)                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1yx9A01 A:1-170 Acid Proteases                                                                                                                                            1yx9A02 A:171-327 Acid Proteases                                                                                                                             CATH domains
               Pfam domains ------------Asp-1yx9A01 A:13-326                                                                                                                                                                                                                                                                                                     - Pfam domains
         Sec.struct. author .eeee.eee...eeeeeeee....eeeeeeee.....eee......hhhhhh....hhhhh...eeeeeeeeee....eeeeeeeeeeeee..eeeeeeeeeeeee...hhhhhh...eeee..hhhhhhhhh.hhhhhhhhh......eeeee.........eeee...hhhhh....eeee.......eeeeeeeee..eeee....eeeee......eeehhhhhhhhhhhhh.ee.....ee...hhhhhh..eeeee..eeeee.....eee....eee.eee..........eeehhhhhh.eeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------PEPTIDASE_A1  PDB: A:14-324 UniProt: 73-382                                                                                                                                                                                                                                                                           --- PROSITE (1)
                PROSITE (2) ----------------------------ASP_PROTEASE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yx9 A   1 IGDEPLENYLDTEYFGTIGIGTPAQDFTVIFDTGSSNLWVPSVYCSSLACSDHNQFNPDDSSTFEATSQELSITYGTGSMTGILGYDTVQVGGISDTNQIFGLSETEPGSFLYYAPFDGILGLAYPSISASGATPVFDNLWDQGLVSQDLFSVYLSSNDDSGSVVLLGGIDSSYYTGSLNWVPVSVEGYWQITLDSITMDGETIACSGGCQAIVDTGTSLLTGPTSAIANIQSDIGASENSDGEMVISCSSIDSLPDIVFTINGVQYPLSPSAYILQDDDSCTSGFEGMDVPTSSGELWILGDVFIRQYYTVFDRANNKVGLAPVA 327
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       231       241       251       261       271       281       291       301       311       321      
                                                                                                                                                                                                                                                              229|                                                                                                
                                                                                                                                                                                                                                                               231
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_AA (368)
(-)
Family: Asp (155)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PEPA_PIG | P00791)
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:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  1yx9
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  3.4.23.1
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PEPA_PIG | P00791: 1f34 1psa 2psg 3pep 3psg 4pep 5pep

(-) Related Entries Specified in the PDB File

4pep 5pep