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Title :  COMPARATIVE MOLECULAR MODEL BUILDING OF TWO SERINE PROTEINASES FROM CYTOTOXIC T LYMPHOCYTES
 
Authors :  M. Murphy, M. N. G. James
Date :  26 Oct 90  (Deposition) - 15 Oct 90  (Release) - 01 Apr 03  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Serine Proteinase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. E. Murphy, J. Moult, R. C. Bleackley, H. Gershenfeld, I. L. Weissman, M. N. James
Comparative Molecular Model Building Of Two Serine Proteinases From Cytotoxic T Lymphocytes.
Proteins V. 4 190 1988
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOTOXIC T-LYMPHOCYTE PROTEINASE I
    ChainsA
    EngineeredYES

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2CP1)

(-) Sites  (0, 0)

(no "Site" information available for 2CP1)

(-) SS Bonds  (3, 3)

Theoretical Model
No.Residues
1A:29 -A:45
2A:122 -A:189
3A:153 -A:168

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Pro A:206 -Pro A:207

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CP1)

(-) PROSITE Motifs  (3, 3)

Theoretical Model (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.GRAB_MOUSE21-245  1A:1-225
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.GRAB_MOUSE60-65  1A:40-45
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.GRAB_MOUSE197-208  1A:177-188

(-) Exons   (0, 0)

(no "Exon" information available for 2CP1)

(-) Sequences/Alignments

Theoretical Model
   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:227
 aligned with GRAB_MOUSE | P04187 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:227
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       
           GRAB_MOUSE    21 IIGGHEVKPHSRPYMALLSIKDQQPEAICGGFLIREDFVLTAAHCEGSIINVTLGAHNIKEQEKTQQVIPMVKCIPHPDYNPKTFSNDIMLLKLKSKAKRTRAVRPLNLPRRNVNVKPGDVCYVAGWGRMAPMGKYSNTLQEVELTVQKDRECESYFKNRYNKTNQICAGDPKTKRASFRGDSGGPLVCKKVAAGIVSYGYKDGSPPRAFTKVSSFLSWIKKTMKSS 247
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee....eeeeeeeeee..eeeehhhhh..eeeeee............eeeeeeeeee.............eeeee..................................eee..eee............hhhhhhh.hhhhhhhh................................................hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:1-225 UniProt: 21-245                                                                                                                                                                                        -- PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cp1 A   1 IIGGHEVKPHSRPYMALLSIKDQQPEAICGGFLIREDFVLTAAHCEGSIINVTLGAHNIKEQEKTQQVIPMVKCIPHPDYNPKTFSNDIMLLKLKSKAKRTRAVRPLNLPRRNVNVKPGDVCYVAGWGRMAPMGKYSNTLQEVELTVQKDRECESYFKNRYNKTNQICAGDPKTKRASFRGDSGGPLVCKKVAAGIVSYGYKDGSPPRAFTKVSSFLSWIKKTMKSS 227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       

   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  (0, 0)

(no "SCOP Domain" information available for 2CP1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CP1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CP1)

(-) Gene Ontology  (15, 15)

Theoretical Model(hide GO term definitions)
Chain A   (GRAB_MOUSE | P04187)
molecular function
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0007219    Notch signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0001913    T cell mediated cytotoxicity    The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0008626    granzyme-mediated apoptotic signaling pathway    A series of molecular signals induced by granzymes which triggers the apoptotic death of a cell. The pathway starts with reception of a granzyme signal, and ends when the execution phase of apoptosis is triggered. Granzymes are serine proteases that are secreted by cytotoxic T cells and natural killer cells to induce apoptosis in target cells.
    GO:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0044194    cytolytic granule    A specialized secretory lysosome that is present in cells with cytolytic capability such as cytotoxic T lymphocytes and natural killer cells. Cytolytic granules mediate the storage and regulated excretion of lytic molecules for killing of target cells.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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    Pro A:206 - Pro A:207   [ RasMol ]  
 

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