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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRYPSIN-LIKE MUTANT (S189D, A226G) CHYMOTRYPSIN.
 
Authors :  B. Jelinek, G. Katona, K. Fodor, I. Venekei, L. Graf
Date :  22 Jan 07  (Deposition) - 18 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Substrate Specificity, Zymogen, Protease, Hydrolase, Digestion, Serine Protease, Protein Engineering (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Jelinek, G. Katona, K. Fodor, I. Venekei, L. Graf
The Crystal Structure Of A Trypsin-Like Mutant Chymotrypsin: The Role Of Position 226 In The Activity And Specificity Of S189D Chymotrypsin.
Protein J. V. 27 79 2008
PubMed-ID: 17805946  |  Reference-DOI: 10.1007/S10930-007-9110-3

(-) Compounds

Molecule 1 - CHYMOTRYPSINOGEN B CHAIN A
    ChainsA
    EC Number3.4.21.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET17B
    Expression System StrainBL21 (DE3) PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDES 19-28
    OrganPANCREAS
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
 
Molecule 2 - CHYMOTRYPSINOGEN B CHAIN B
    ChainsB
    EC Number3.4.21.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET17B
    Expression System StrainBL21 (DE3) PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 37-164
    OrganPANCREAS
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
 
Molecule 3 - CHYMOTRYPSINOGEN B CHAIN C
    ChainsC
    EC Number3.4.21.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET17B
    Expression System StrainBL21 (DE3) PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 165-263
    MutationYES
    OrganPANCREAS
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2JET)

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:1 -B:122
2B:42 -B:58
3B:136 -C:201
4C:168 -C:182
5C:191 -C:220

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JET)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CTRB1_RAT71-76  1B:53-58
2TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CTRB1_RAT207-218  1C:190-200

(-) Exons   (0, 0)

(no "Exon" information available for 2JET)

(-) 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:12
 aligned with CTRB1_RAT | P07338 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:15
                                    23     
            CTRB1_RAT    14 GATFGCGVPTIQPVL  28
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author ..---.......... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 2jet A  -1 QA---CGVPTIQPVL  10
                             |   |   5     
                             0   1         

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with CTRB1_RAT | P07338 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:128
                                    46        56        66        76        86        96       106       116       126       136       146       156        
            CTRB1_RAT    37 GEDAIPGSWPWQVSLQDKTGFHFCGGSLISEDWVVTAAHCGVKTSDVVVAGEFDQGSDEENIQVLKIAQVFKNPKFNMFTVRNDITLLKLATPAQFSETVSAVCLPNVDDDFPPGTVCATTGWGKTKY 164
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2jetB00 B:19-146 Trypsin-like serine proteases                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........eeeee.....eeeeeee....eeee..........eeee......---...eeeeeeeeee.............eeeee..........................eeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------TRYPSI---------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jet B  19 GEDAIPGSWPWQVSLQDKTGFHFCGGSLISEDWVVTAAHCGVKTSDVVVAGEFDQG---ENIQVLKIAQVFKNPKFNMFTVRNDITLLKLATPAQFSETVSAVCLPNVDDDFPPGTVCATTGWGKTKY 146
                                    28        38        48        58        68     |  78        88        98       108       118       128       138        
                                                                                  74  78                                                                    

Chain C from PDB  Type:PROTEIN  Length:93
 aligned with CTRB1_RAT | P07338 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:93
                                   178       188       198       208       218       228       238       248       258   
            CTRB1_RAT   169 TPEKLQQAALPIVSEADCKKSWGSKITDVMTCAGASGVSSCMGDSGGPLVCQKDGVWTLAGIVSWGSGVCSTSTPAVYSRVTALMPWVQQILE 261
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2jetC00 C:151-243 Trypsin-like serine proteases                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeehhhhhhhhh.......eeee.....hhhhh....eeeee....eeeeeeeee..........eeeeehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------TRYPSIN_SER ------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 2jet C 151 TPEKLQQAALPIVSEADCKKSWGSKITDVMTCAGASGVDSCMGDSGGPLVCQKDGVWTLAGIVSWGSGVCSTSTPGVYSRVTALMPWVQQILE 243
                                   160       170       180       190       200       210       220       230       240   

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 2JET)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (CTRB1_RAT | P07338)
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: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:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    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.
    GO:0034097    response to cytokine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
    GO:0032094    response to food    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a food stimulus; food is anything which, when taken into the body, serves to nourish or build up the tissues or to supply body heat.
    GO:0007584    response to nutrient    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
    GO:0043434    response to peptide hormone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CTRB1_RAT | P073381kdq

(-) Related Entries Specified in the PDB File

1kdq CRYSTAL STRUCTURE ANALYSIS OF THE MUTANT S189D RATCHYMOTRYPSIN