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(-) Description

Title :  STRUCTURE OF PEROXISOMAL TARGETING SIGNAL 1 (PTS1) BINDING DOMAIN OF TRYPANOSOMA BRUCEI PEROXIN 5 (TBPEX5)COMPLEXED TO T. BRUCEI PHOSPHOGLUCOISOMERASE (PGI) PTS1 PEPTIDE
 
Authors :  P. Sampathkumar, C. Roach, P. A. M Michels, W. G. J. Hol
Date :  17 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: UNP RESIDUES 332-655
    Gene: PEX5
    Mutation: YES
    Organism Scientific: TRYPANOSOMA BRUCEI
 
Molecule 2 - T. BRUCEI PGI PTS1 PEPTIDE AC-FNELSHL
    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  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1EDO12Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:625BINDING SITE FOR RESIDUE EDO A 1
02AC2SOFTWAREARG A:549 , PRO A:550 , GLN A:551 , GLU A:552BINDING SITE FOR RESIDUE EDO A 2
03AC3SOFTWAREGLU A:350 , ASN A:351 , GLU A:354 , GLU A:355BINDING SITE FOR RESIDUE EDO A 4
04AC4SOFTWAREARG A:410 , HIS A:420 , LEU A:423 , ALA A:435 , SER A:439 , ALA A:442BINDING SITE FOR RESIDUE EDO A 5
05AC5SOFTWAREALA A:394 , ASN A:538 , TYR A:567 , ARG A:569 , LEU B:7BINDING SITE FOR RESIDUE EDO A 6
06AC6SOFTWAREGLN A:535 , LYS A:539BINDING SITE FOR RESIDUE EDO A 7
07AC7SOFTWAREASN A:511 , ASN A:514 , TYR A:516BINDING SITE FOR RESIDUE EDO A 8
08AC8SOFTWAREARG A:621 , ASN A:625 , TYR A:637BINDING SITE FOR RESIDUE EDO A 9
09AC9SOFTWAREGLN A:501 , ALA A:504 , SER A:505 , LYS A:539BINDING SITE FOR RESIDUE EDO A 10
10BC1SOFTWAREGLY A:329 , GLU A:381BINDING SITE FOR RESIDUE EDO A 11
11BC2SOFTWARELEU A:360 , LEU A:391 , GLU A:395BINDING SITE FOR RESIDUE EDO A 12

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CV0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CV0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CV0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CV0)

(-) Exons   (0, 0)

(no "Exon" information available for 3CV0)

(-) 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:300
 aligned with Q57W55_TRYB2 | Q57W55 from UniProtKB/TrEMBL  Length:655

    Alignment length:370
                                   293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653
         Q57W55_TRYB2   284 DHMQGQDGVQRGTDEDMEGMMGDDVYDPSADVEQWAQEYAQMQAMQERLQNNTDYPFEANNPYMYHENPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEPFAKEFGLQSM 653
               SCOP domains d3c                                             v0a_ 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....-----..hhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cv0 A 329 GHM---------------------------------------------LQNNTDYPFEANNPYMYHENPMEEGLSMLKLANLAEAALAFEAVCQAAPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQL--------------------FFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTT-----SREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEPFAKEFGLQSM 653
                              |      -         -         -         -       333       343       353       363       373       383       393       403       413       423       433       443       453         -         -|      483       493       503       513       523       533       543       553       563       573       583       593       603     | 613       623       633       643       653
                            331                                           332                                                                                                                      453                  474                                                                                                                              603   609                                            


Chain A from PDB  Type:PROTEIN  Length:300
 aligned with Q9U7C3_9TRYP | Q9U7C3 from UniProtKB/TrEMBL  Length:655

    Alignment length:370
                                   293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653
         Q9U7C3_9TRYP   284 DHMQGQDGVQRGTDEDMEGMMGDDVYDPSADVEQWAQEYAQMQAMQERLQNNTDYPFEANNPYMYHENPMEEGLSMLKLANLAEAALAFEAVCQKEPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQLGSVNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTTPTGEASREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEPFAKEFGLQSM 653
               SCOP domains d3c                                             v0a_ 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....-----..hhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cv0 A 329 GHM---------------------------------------------LQNNTDYPFEANNPYMYHENPMEEGLSMLKLANLAEAALAFEAVCQAAPEREEAWRSLGLTQAENEKDGLAIIALNHARMLDPKDIAVHAALAVSHTNEHNANAALASLRAWLLSQPQYEQL--------------------FFFAAPNEYRECRTLLHAALEMNPNDAQLHASLGVLYNLSNNYDSAAANLRRAVELRPDDAQLWNKLGATLANGNRPQEALDAYNRALDINPGYVRVMYNMAVSYSNMSQYDLAAKQLVRAIYMQVGGTT-----SREATRSMWDFFRMLLNVMNRPDLVELTYAQNVEPFAKEFGLQSM 653
                              |      -         -         -         -       333       343       353       363       373       383       393       403       413       423       433       443       453         -         -|      483       493       503       513       523       533       543       553       563       573       583       593       603     | 613       623       633       643       653
                            331                                           332                                                                                                                      453                  474                                                                                                                              603   609                                            


Chain B from PDB  Type:PROTEIN  Length:6
 aligned with G6PI_TRYBB | P13377 from UniProtKB/Swiss-Prot  Length:607

    Alignment length:6
           G6PI_TRYBB   602 NELSHL 607
               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
                 3cv0 B   2 NELSHL   7
   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 3CV0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CV0)

(-) Gene Ontology  (11, 11)

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)

Chain B   (G6PI_TRYBB | P13377)
molecular function
    GO:0004347    glucose-6-phosphate isomerase activity    Catalysis of the reaction: D-glucose 6-phosphate = D-fructose 6-phosphate.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
cellular component
    GO:0020015    glycosome    A membrane-bounded organelle found in organisms from the order Kinetoplastida that houses the enzymes of glycolysis.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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 Related Entries

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

UniProtKB/Swiss-Prot
        G6PI_TRYBB | P13377: 2aol 2o2c 2o2d
        Q57W55_TRYB2 | Q57W55: 3cvn
        Q9U7C3_9TRYP | Q9U7C3: 3cvp 3cvq
UniProtKB/TrEMBL
        Q57W55_TRYB2 | Q57W55: 3cvp 3cvq
        Q9U7C3_9TRYP | Q9U7C3: 1hxi 3cvl 3cvn

(-) Related Entries Specified in the PDB File

3cvl SAME PROTEIN COMPLEXED WITH T.BRUCEI PHOSPHOFRUCTO KINASE (TBPFK) PTS1 PEPTIDE
3cvn SAME PROTEIN COMPLEXED TO T. BRUCEI GLYCERALDEHYDE-3- PHOSPHATE DEHYDROGENASE (TBGAPDH) PTS1 PEPTIDE
3cvp SAME PROTEIN COMPLEX WITH PTS1 PEPTIDE (10-SKL WITH THE SEQUENCE ACGTLSNRASKL)
3cvq SAME PROTEIN COMPLEX WITH PTS1 PEPTIDE (7-SKL WITH THE SEQUENCE SNRWSKL)