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(-) Description

Title :  SOLUTION STRUCTURE OF THE SCPEX13P SH3 DOMAIN
 
Authors :  J. R. Pires, X. Hong, C. Brockmann, R. Volkmer-Engert, J. Schneider- Mergener, H. Oschkinat, R. Erdmann
Date :  09 Jan 03  (Deposition) - 04 Mar 03  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Yeast, Membrane Protein, Pex5P, Pex14P, Pex13P, Import Machine, Sh3 Domain, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Pires, X. Hong, C. Brockmann, R. Volkmer-Engert, J. Schneider-Mergener, H. Oschkinat, R. Erdmann
The Scpex13P Sh3 Domain Exposes Two Distinct Binding Sites For Pex5P And Pex14P
J. Mol. Biol. V. 326 1427 2003
PubMed-ID: 12595255  |  Reference-DOI: 10.1016/S0022-2836(03)00039-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXISOMAL MEMBRANE PROTEIN PAS20
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-4T2
    Expression System Strain: BL21-DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SH3 DOMAIN
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: PEX13P SH3 DOMAIN

 Structural Features

(-) Chains, Units

  
NMR Structure (10x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1NM7)

(-) Sites  (0, 0)

(no "Site" information available for 1NM7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NM7)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NM7)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YLR191W1YLR191W.1XII:537274-5384341161PEX13_YEAST1-3863861A:310-37061

(-) Sequences/Alignments

NMR Structure
   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:61
 aligned with PEX13_YEAST | P80667 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:61
                                   319       329       339       349       359       369 
          PEX13_YEAST   310 FARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEII 370
               SCOP domains d1nm7a_ A: Peroxisomal membrane protein Pex13p                SCOP domains
               CATH domains 1nm7A00 A:310-370 SH3 Domains                                 CATH domains
               Pfam domains --SH3_1-1nm7A01 A:312-364                              ------ Pfam domains
         Sec.struct. author .eee...................eeee.............eeeee...eeeeehhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:310-370 UniProt: 1-386 [INCOMPLETE]          Transcript 1
                 1nm7 A 310 FARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEII 370
                                   319       329       339       349       359       369
   Legend:   → Mismatch (orange background)
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  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)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: SH3 (175)

(-) Gene Ontology  (11, 11)

NMR Structure(hide GO term definitions)
Chain A   (PEX13_YEAST | P80667)
molecular function
    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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
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.
    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:1990415    Pex17p-Pex14p docking complex    A protein complex involved in the peroxisomal import machinery. In S. cerevisiae, this complex contains the proteins Pex17p, Pex14p, Pex19, and Pex13p.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:1990429    peroxisomal importomer complex    A protein complex responsible for transporting proteins into the peroxisomal matrix. An example of this complex is Pex14 found in S. cerevisae which has 9 core components and 12 transient interaction partners.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PEX13_YEAST | P80667: 1jqq 1n5z 2v1r

(-) Related Entries Specified in the PDB File

1n5z 1N5Z CONTAINS COMPLEX STRUCTURE OF PEX13P SH3 DOMAIN WITH A PEPTIDE OF PEX14P