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(-) Description

Title :  A NOVEL CONFORMATION FOR THE TPR DOMAIN OF PEX5P
 
Authors :  W. A. Stanley, M. Wilmanns, P. Kursula
Date :  15 Nov 06  (Deposition) - 17 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transport, Zellweger Syndrome, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. A. Stanley, N. Pursiainen, E. F. Garman, A. Juffer, M. Wilmanns, P. Kursula
A Previously Unobserved Conformation For The Human Pex5P Receptor Suggests Roles For Intrinsic Flexibility And Rigid Domain Motions In Ligand Binding
Bmc Struct. Biol. V. 7 24 2007
PubMed-ID: 17428317  |  Reference-DOI: 10.1186/1472-6807-7-24

(-) Compounds

Molecule 1 - PEROXISOMAL TARGETING SIGNAL 1 RECEPTOR
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24D
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentTPR DOMAIN, RESIDUES 278-602
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPEX5P, PEROXISOME RECEPTOR 1, PEROXISOMAL C-TERMINAL TARGETING SIGNAL IMPORT RECEPTOR, PTS1-BP, PEROXIN-5, PTS1 RECEPTOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SR2Ligand/IonSTRONTIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:479 , ASP A:482 , SER A:485 , HOH A:2006BINDING SITE FOR RESIDUE SR A1640
2AC2SOFTWAREVAL B:479 , ASP B:482 , SER B:485 , HOH B:2001 , HOH B:2002 , HOH B:2003BINDING SITE FOR RESIDUE SR B1640

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J9Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2J9Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric/Biological Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_007543N526KPEX5_HUMANDisease (PBD2B)61752138A/BN526K
2UniProtVAR_031328S600WPEX5_HUMANDisease (PBD2B)  ---A/BS600W

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

(-) PROSITE Motifs  (2, 10)

Asymmetric/Biological Unit (2, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TPRPS50005 TPR repeat profile.PEX5_HUMAN335-368
369-402
 
488-521
 
522-555
 
556-589
 
  9A:335-368
A:369-402
B:369-402
A:488-521
B:488-521
A:522-555
B:522-555
A:556-589
B:556-589
2TPR_REGIONPS50293 TPR repeat region circular profile.PEX5_HUMAN335-589  1A:335-589

(-) Exons   (0, 0)

(no "Exon" information available for 2J9Q)

(-) 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 PEX5_HUMAN | P50542 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:417
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       
           PEX5_HUMAN   223 GEGQVSLESGAGSGRAQAEQWAAEFIQQQGTSDAWVDQFTRPVNTSALDMEFERAKSAIESDVDFWDKLQAELEEMAKRDAEAHPWLSDYDDLTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACETLRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAADARDLSTLLTMFGLPQ 639
               SCOP domains d2j                                                                                         9qa_ A: automated matches                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...-----------------------------------------------------------------------------------------......................hhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhh..-----------------------hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.-----hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K-------------------------------------------------------------------------W--------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------------------------------------------------------------------------------------------------TPR  PDB: A:335-368               TPR  PDB: A:369-402               -------------------------------------------------------------------------------------TPR  PDB: A:488-521               TPR  PDB: A:522-555               TPR  PDB: A:556-589               -------------------------------------------------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------TPR_REGION  PDB: A:335-589 UniProt: 335-589                                                                                                                                                                                                                    -------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j9q A 312 GMG-----------------------------------------------------------------------------------------LTSATYDKGYQFEEENPLRDHPQPFEEGLRRLQEGDLPNAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTP-----------------------SLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRG-----GAMSENIWSTLRLALSMLGQSDAYGAADARDLSTLLTMFGLPQ 639
                              |      -         -         -         -         -         -         -         -         -  |    322       332       342       352       362       372       382       392       402       412       422       432       442         -         -   |   472       482       492       502       512       522       532       542       552       562       572       582        |-    |  602       612       622       632       
                              |                                                                                       315                                                                                                                            442                     466                                                                                                                          591   597                                          
                            314                                                                                                                                                                                                                                                                                                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:269
 aligned with PEX5_HUMAN | P50542 from UniProtKB/Swiss-Prot  Length:639

    Alignment length:287
                                   362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       
           PEX5_HUMAN   353 NAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACETLRDWLRYTPAYAHLVTPAEEGAGGAGLGPSKRILGSLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAADARDLSTLLTMFGLPQ 639
               SCOP domains d2j9qb_ B: automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....------------------....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------K-------------------------------------------------------------------------W--------------------------------------- SAPs(SNPs)
                PROSITE (1) TPR  PDB: -     TPR  PDB: B:369-402               -------------------------------------------------------------------------------------TPR  PDB: B:488-521               TPR  PDB: B:522-555               TPR  PDB: B:556-589               -------------------------------------------------- PROSITE (1)
                PROSITE (2) TPR_REGION  PDB: - UniProt: 335-589                                                                                                                                                                                                          -------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j9q B 353 NAVLLFEAAVQQDPKHMEAWQYLGTTQAENEQELLAISALRRCLELKPDNQTALMALAVSFTNESLQRQACEILRDWLRYTPAYAHLVTP------------------SLLSDSLFLEVKELFLAAVRLDPTSIDPDVQCGLGVLFNLSGEYDKAVDCFTAALSVRPNDYLLWNKLGATLANGNQSEEAVAAYRRALELQPGYIRSRYNLGISCINLGAHREAVEHFLEALNMQRKSRGPRGEGGAMSENIWSTLRLALSMLGQSDAYGAADARDLSTLLTMFGLPQ 639
                                   362       372       382       392       402       412       422       432       442         -       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       
                                                                                                                   442                461                                                                                                                                                                                  

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2J9Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J9Q)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PEX5_HUMAN | P50542)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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:0000268    peroxisome targeting sequence binding    Interacting selectively and non-covalently with a peroxisomal targeting sequence, any of several sequences of amino acids within a protein that can act as a signal for the localization of the protein into the peroxisome.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0031267    small GTPase binding    Interacting selectively and non-covalently with a small monomeric GTPase.
biological process
    GO:1901094    negative regulation of protein homotetramerization    Any process that stops, prevents or reduces the frequency, rate or extent of protein homotetramerization.
    GO:0016558    protein import into peroxisome matrix    The import of proteins into the peroxisomal matrix. A peroxisome targeting signal (PTS) binds to a soluble receptor protein in the cytosol, and the resulting complex then binds to a receptor protein in the peroxisome membrane and is imported. The cargo protein is then released into the peroxisome matrix.
    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.
    GO:0016561    protein import into peroxisome matrix, translocation    The process in which proteins are moved across the peroxisomal membrane into the matrix. It is likely that the peroxisome targeting sequence receptor remains associated with cargo proteins during translocation.
    GO:0045046    protein import into peroxisome membrane    The targeting of proteins into the peroxisomal membrane. The process is not well understood, but both signals and mechanism differ from those involved in peroxisomal matrix protein import.
    GO:0006625    protein targeting to peroxisome    The process of directing proteins towards the peroxisome, usually using signals contained within the protein.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005782    peroxisomal matrix    The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.
    GO:0005778    peroxisomal membrane    The lipid bilayer surrounding a peroxisome.
    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.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PEX5_HUMAN | P505421fch 2c0l 2c0m 2w84 3r9a 4bxu 4kxk 4kyo

(-) Related Entries Specified in the PDB File

1fch CRYSTAL STRUCTURE OF THE PTS1 COMPLEXED TO THE TPR REGIONOF HUMAN PEX5
2c0l TPR DOMAIN OF HUMAN PEX5P IN COMPLEX WITH HUMAN MSCP2
2c0m APO FORM OF THE TPR DOMAIN OF THE PEX5P RECEPTOR