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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ACTIVATION INTERMEDIATE OF CATHEPSIN E
 
Authors :  N. Ostermann, B. Gerhartz, S. Worpenberg, J. Trappe, J. Eder
Date :  12 Jul 04  (Deposition) - 12 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,P,X
Biol. Unit 1:  A,P,X  (2x)
Keywords :  Hydrolase, Aspartic Protease, Activation Intermediate (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Ostermann, B. Gerhartz, S. Worpenberg, J. Trappe, J. Eder
Crystal Structure Of An Activation Intermediate Of Cathepsin E
J. Mol. Biol. V. 342 889 2004
PubMed-ID: 15342244  |  Reference-DOI: 10.1016/J.JMB.2004.07.073
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CATHEPSIN E
    ChainsA
    EC Number3.4.23.34
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - ACTIVATION PEPTIDE FROM CATHEPSIN E
    ChainsP
    EC Number3.4.23.34
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - 23-MER PEPTIDE FROM PELB-IGG KAPPA LIGHT CHAIN FUSION PROTEIN
    ChainsX
    EngineeredYES
    Other DetailsTHE SEQUENCE OCCURS PEPTIDE SYNTHESIS
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit APX
Biological Unit 1 (2x)APX

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1TZS)

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:56 -A:61
2A:219 -A:223
3A:261 -A:298

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:33 -Pro A:34
2Asn A:169 -Pro A:170
3Pro A:309 -Pro A:310
4Gly A:312 -Pro A:313

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_061731I82VCATE_HUMANPolymorphism57621203AI29V
2UniProtVAR_014572T329ICATE_HUMANPolymorphism6503AT271I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_061731I82VCATE_HUMANPolymorphism57621203AI29V
2UniProtVAR_014572T329ICATE_HUMANPolymorphism6503AT271I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 3)

Asymmetric Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.CATE_HUMAN78-397  1A:25-339
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.CATE_HUMAN93-104
283-294
  2A:40-51
A:225-236
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.CATE_HUMAN78-397  2A:25-339
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.CATE_HUMAN93-104
283-294
  4A:40-51
A:225-236

(-) Exons   (0, 0)

(no "Exon" information available for 1TZS)

(-) Sequences/Alignments

Asymmetric 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:322
 aligned with CATE_HUMAN | P14091 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:334
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396    
           CATE_HUMAN    67 KEPLINYLDMEYFGTISIGSPPQNFTVIFDTGSSNLWVPSVYCTSPACKTHSRFQPSQSSTYSQPGQSFSIQYGTGSLSGIIGADQVSAFATQVEGLTVVGQQFGESVTEPGQTFVDAEFDGILGLGYPSLAVGGVTPVFDNMMAQNLVDLPMFSVYMSSNPEGGAGSELIFGGYDHSHFSGSLNWVPVTKQAYWQIALDNIQVGGTVMFCSEGCQAIVDTGTSLITGPSDKIKQLQNAIGAAPVDGEYAVECANLNVMPDVTFTINGVPYTLSPTAYTLLDFVDGMQFCSSGFQGLDIHPPAGPLWILGDVFIRQFYSVFDRGNNRVGLAPAV 400
               SCOP domains d1tzsa_ A: automated matches                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------Asp-1tzsA01 A:24-341                                                                                                                                                                                                                                                                                                               - Pfam domains
         Sec.struct. author ...hhhhh.....eeeee....eeeeeeee.....eeee.....hhhhh.....hhhhh........eeeee....eeeeeeeeeeee-----e..eeeeeeeeeee....hhhhhhh...eeee..hhhhhhhhh.hhhhhhhhh......eeeee.....--....eeee...hhhhh....eeee.......eeeeeeeee..eeee....eeeee......eeehhhhhhhhhhhhh.ee....eeehhhhhhhh..eeeee..eeeee.....ee..-----..eee.eee..........eeehhhhhhheeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I----------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------PEPTIDASE_A1  PDB: A:25-339 UniProt: 78-397                                                                                                                                                                                                                                                                                     --- PROSITE (1)
                PROSITE (2) --------------------------ASP_PROTEASE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE---------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tzs A  14 KEPLINYLDMEYFGTISIGSPPQNFTVIFDTGSSNLWVPSVYCTSPACKTHSRFQPSQSSTYSQPGQSFSIQYGTGSLSGIIGADQVS-----VEGLTVVGQQFGESVTEPGQTFVDAEFDGILGLGYPSLAVGGVTPVFDNMMAQNLVDLPMFSVYMSSNP--GAGSELIFGGYDHSHFSGSLNWVPVTKQAYWQIALDNIQVGGTVMFCSEGCQAIVDTGTSLITGPSDKIKQLQNAIGAAPVDGEYAVECANLNVMPDVTFTINGVPYTLSPTAYTLLD-----QFCSSGFQGLDIHPPAGPLWILGDVFIRQFYSVFDRGNNRVGLAPAV 342
                                    23        33        43        53        63        73        83        93       | -   |   108       118       128       138       148       158       168 |  |  178       188       198       208       218       228       238       248       258       268       278       288 |     298       308       318       328       338    
                                                                                                                 101   102                                                                 170  |                                                                                                                  290   296                                              
                                                                                                                                                                                              173                                                                                                                                                                         

Chain P from PDB  Type:PROTEIN  Length:9
 aligned with CATE_HUMAN | P14091 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:9
           CATE_HUMAN    19 GSLHRVPLR  27
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --A1_Prop Pfam domains
         Sec.struct. author ...eeee.. Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                PROSITE (1) --------- PROSITE (1)
                PROSITE (2) --------- PROSITE (2)
                 Transcript --------- Transcript
                 1tzs P   1 GSLHRVPLR   9

Chain X from PDB  Type:PROTEIN  Length:5
                                     
               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
                 1tzs X  19 PAMAM  23

   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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1TZS)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Family: Asp (155)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,P   (CATE_HUMAN | P14091)
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.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0019886    antigen processing and presentation of exogenous peptide antigen via MHC class II    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
    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:0016540    protein autoprocessing    Processing which a protein carries out itself. This involves actions such as the autolytic removal of residues to generate the mature form of the protein.
    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:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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    Asn A:169 - Pro A:170   [ RasMol ]  
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