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(-) Description

Title :  STRUCTURE OF PEROXISOMAL TARGETING SIGNAL 1 (PTS1) BINDING DOMAIN OF TRYPANOSOMA BRUCEI PEROXIN 5 (TBPEX5)COMPLEXED TO PTS1 PEPTIDE (10-SKL)
 
Authors :  P. Sampathkumar, C. Roach, P. A. M Michels, W. G. J. Hol
Date :  18 Apr 08  (Deposition) - 24 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tpr Motifs, Tpr Protein, Peroxin 5, Pex5, Pts1 Binding Domain, Protein-Peptide Complex, Receptor, Tpr Repeat, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Sampathkumar, C. Roach, P. A. Michels, W. G. Hol
Structural Insights Into The Recognition Of Peroxisomal Targeting Signal 1 By Trypanosoma Brucei Peroxin 5.
J. Mol. Biol. V. 381 867 2008
PubMed-ID: 18598704  |  Reference-DOI: 10.1016/J.JMB.2008.05.089
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXISOME TARGETING SIGNAL 1 RECEPTOR PEX5
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSKB3
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Fragment: PEROXISOMAL TARGETING SINGAL 1 (PTS1) BINDING DOMAIN OF TBPEX5
    Gene: PEX5
    Mutation: YES
    Organism Scientific: TRYPANOSOMA BRUCEI
 
Molecule 2 - 10-SKL PTS1 PEPTIDE AC-GTLSNRASKL
    Chains: B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3CVP)

(-) Sites  (0, 0)

(no "Site" information available for 3CVP)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CVP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CVP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CVP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CVP)

(-) Exons   (0, 0)

(no "Exon" information available for 3CVP)

(-) 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:279
 aligned with Q57W55_TRYB2 | Q57W55 from UniProtKB/TrEMBL  Length:655

    Alignment length:313
                                   345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645   
         Q57W55_TRYB2   336 TDYPFEANNPYMYHENPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEPFAKEF 648
               SCOP domains d3cvpa_ A: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......---------------------....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh-------------................hhhhhhhhhhh.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cvp A 336 TDYPFEANNPYMYHENPMEEGLSMLKLANLAEAALAFEAVCQAAPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQ---------------------FFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQV-------------TRSMWDFFRMLLNVMNRPDLVELTYAQNVEPFAKEF 648
                                   345       355       365       375       385       395       405       415       425       435       445      |  -         -       475       485       495       505       515       525       535       545       555       565       575       585       595   |     -       615       625       635       645   
                                                                                                                                              452                   474                                                                                                                          599           613                                   


Chain A from PDB  Type:PROTEIN  Length:279
 aligned with Q9U7C3_9TRYP | Q9U7C3 from UniProtKB/TrEMBL  Length:655

    Alignment length:313
                                   345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645   
         Q9U7C3_9TRYP   336 TDYPFEANNPYMYHENPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEPFAKEF 648
               SCOP domains d3cvpa_ A: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......---------------------....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh-------------................hhhhhhhhhhh.hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cvp A 336 TDYPFEANNPYMYHENPMEEGLSMLKLANLAEAALAFEAVCQAAPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQ---------------------FFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQV-------------TRSMWDFFRMLLNVMNRPDLVELTYAQNVEPFAKEF 648
                                   345       355       365       375       385       395       405       415       425       435       445      |  -         -       475       485       495       505       515       525       535       545       555       565       575       585       595   |     -       615       625       635       645   
                                                                                                                                              452                   474                                                                                                                          599           613                                   


Chain B from PDB  Type:PROTEIN  Length:6
                                      
               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
                 3cvp B   5 NRASKL  10
   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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3CVP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CVP)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9U7C3_9TRYP | Q9U7C3)

Chain A   (Q57W55_TRYB2 | Q57W55)
molecular function
    GO:0005052    peroxisome matrix targeting signal-1 binding    Interacting selectively and non-covalently with a type 1 peroxisome targeting signal, a tripeptide with the consensus sequence (S/A/C)-(K/R/H)-L.
    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).
biological process
    GO:0016560    protein import into peroxisome matrix, docking    The process in which a complex formed of a peroxisome targeting sequence (PTS) receptor bound to a PTS-bearing protein docks with translocation machinery in the peroxisomal membrane.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005778    peroxisomal membrane    The lipid bilayer surrounding a peroxisome.

 Visualization

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(no "Cis Peptide Bonds" information available for 3cvp)
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q57W55_TRYB2 | Q57W55: 3cvn
        Q9U7C3_9TRYP | Q9U7C3: 3cv0 3cvq
UniProtKB/TrEMBL
        Q57W55_TRYB2 | Q57W55: 3cv0 3cvq
        Q9U7C3_9TRYP | Q9U7C3: 1hxi 3cvl 3cvn

(-) Related Entries Specified in the PDB File

3cv0 SAME PROTEIN COMPLEXED TO T. BRUCEI PHOSPHOGLUCOISOMERASE (TBPGI) PTS1 PEPTIDE
3cvl SAME PROTEIN COMPLEXED TO T. BRUCEI PHOSPHOFRUCTOKINASE (TBPFK) PTS1 PEPTIDE
3cvn SAME PROTEIN COMPLEXED TO T. BRUCEI GLYCERALDEHYDE-3- PHOSPHATE DEHYDROGENASE (TBGAPDH) PTS1 PEPTIDE
3cvq SAME PROTEIN COMPLEX WITH PTS1 PEPTIDE (7-SKL WITH THE SEQUENCE SNRWSKL)