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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 (7-SKL)
 
Authors :  P. Sampathkumar, C. Roach, P. A. M. Michels, W. G. J. Hol
Date :  18 Apr 08  (Deposition) - 24 Jun 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.01
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

(-) 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: BINDING DOMAIN,UNP RESIDUES 332-655
    Gene: PEX5
    Mutation: YES
    Organism Scientific: TRYPANOSOMA BRUCEI
 
Molecule 2 - PTS1 PEPTIDE 7-SKL (AC-SNRWSKL)
    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  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SAC1Mod. Amino AcidN-ACETYL-SERINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:596BINDING SITE FOR RESIDUE GOL A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CVQ)

(-) 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:289
 aligned with Q57W55_TRYB2 | Q57W55 from UniProtKB/TrEMBL  Length:655

    Alignment length:315
                                   344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644     
         Q57W55_TRYB2   335 NTDYPFEANNPYMYHENPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEPFAKEFG 649
               SCOP domains d3cvqa_ A: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhh..--------------......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh------------...hhhhhhhhhhhhh.hhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cvq A 335 NTDYPFEANNPYMYHENPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARALDPADIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQLGSVN--------------EDFFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQV------------ATRSMWDFFRMLLNVMNRPDLVELTYAQNVEPFAKEFG 649
                                   344       354       364       374       384       394       404       414       424       434       444       454  |      -       474       484       494       504       514       524       534       544       554       564       574       584       594    |    -       614       624       634       644     
                                                                                                                                                    457            472                                                                                                                            599          612                                     


Chain A from PDB  Type:PROTEIN  Length:289
 aligned with Q9U7C3_9TRYP | Q9U7C3 from UniProtKB/TrEMBL  Length:655

    Alignment length:315
                                   344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644     
         Q9U7C3_9TRYP   335 NTDYPFEANNPYMYHENPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEPFAKEFG 649
               SCOP domains d3cvqa_ A: Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)                                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhh..--------------......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh------------...hhhhhhhhhhhhh.hhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cvq A 335 NTDYPFEANNPYMYHENPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARALDPADIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQLGSVN--------------EDFFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQV------------ATRSMWDFFRMLLNVMNRPDLVELTYAQNVEPFAKEFG 649
                                   344       354       364       374       384       394       404       414       424       434       444       454  |      -       474       484       494       504       514       524       534       544       554       564       574       584       594    |    -       614       624       634       644     
                                                                                                                                                    457            472                                                                                                                            599          612                                     


Chain B from PDB  Type:PROTEIN  Length:7
                                       
               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
                 3cvq B   1 sNRWSKL   7
                            |      
                            1-SAC
   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 3CVQ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
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.

Chain A   (Q9U7C3_9TRYP | Q9U7C3)

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

(-) Related Entries Specified in the PDB File

3cv0 SAME PROTEIN COMPLEX WITH T. BRUCEI PHOSPHOGLUCOISOMERASE (TBPGI) PTS1 PEPTIDE
3cvl SAME PROTEIN COMPLEX WITH T. BRUCEI PHOSPHOFRUCTOKINASE (TBPFK) PTS1 PEPTIDE
3cvn SAME PROTEIN COMPLEX WITH T. BRUCEI GLYCERALDEHYDE-3- PHOSPHATE DEHYROGENASE (TBGAPDH) PTS1 PEPTIDE
3cvp SAME PROTEIN COMPLEX WITH PTS1 PEPTIDE (10-SKL WITH THE SEQUENCE ACGTLSNRASKL)