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(-) Description

Title :  COMPLEX STRUCTURE OF PEX13P SH3 DOMAIN WITH A PEPTIDE OF PEX14P
 
Authors :  A. Douangamath, F. V. Filipp, A. T. J. Klein, P. Barnett, P. Zou, T. Voorn-Brouwer, M. C. Vega, O. M. Mayans, M. Sattler, B. Distel, M. Wilmanns
Date :  08 Nov 02  (Deposition) - 11 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,P,Q
Biol. Unit 1:  A,P  (1x)
Biol. Unit 2:  B,Q  (1x)
Biol. Unit 3:  A (1x),B (1x),P (1x),Q (1x)
Biol. Unit 4:  A (1x),B (1x),P (1x),Q (1x)
Keywords :  Sh3 Domain, Pxxp Motif, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Douangamath, F. V. Filipp, A. T. J. Klein, P. Barnett, P. Zou, T. Voorn-Brouwer, M. C. Vega, O. M. Mayans, M. Sattler, B. Distel, M. Wilmanns
Topography For Independent Binding Of Alpha-Helical And Ppii-Helical Ligands To A Peroxisomal Sh3 Domain
Mol. Cell V. 10 1007 2002
PubMed-ID: 12453410  |  Reference-DOI: 10.1016/S1097-2765(02)00749-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEROXISOMAL MEMBRANE PROTEIN PAS20
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMALC2
    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: PEROXIN-13, PEX13
 
Molecule 2 - 14-MER PEPTIDE FROM PEROXISOMAL MEMBRANE PROTEIN PEX14
    Chains: P, Q
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED. THIS SEQUENCE OCCURS NATURALLY IN SACCHAROMYCES CEREVISIAE.
    Synonym: PEROXIN-14
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABPQ
Biological Unit 1 (1x): A P 
Biological Unit 2 (1x):  B Q
Biological Unit 3 (1x): A (1x)B (1x)P (1x)Q (1x)
Biological Unit 4 (1x): A (1x)B (1x)P (1x)Q (1x)

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1N5Z)

(-) Sites  (0, 0)

(no "Site" information available for 1N5Z)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N5Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N5Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N5Z)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.PEX13_YEAST306-372
 		  2A:12-77
B:12-78
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.PEX13_YEAST306-372
 		  1A:12-77
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.PEX13_YEAST306-372
 		  1-
B:12-78
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.PEX13_YEAST306-372
 		  2A:12-77
B:12-78
Biological Unit 4 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.PEX13_YEAST306-372
 		  2A:12-77
B:12-78

(-) Exons   (2, 4)

Asymmetric Unit (2, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGL153W1YGL153W.1VII:216278-2173031026PEX14_YEAST1-3413412P:3-12
Q:3-12		10
10
2.1YLR191W1YLR191W.1XII:537274-5384341161PEX13_YEAST1-3863862A:7-77
B:11-79		71
69

(-) Sequences/Alignments

Asymmetric 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:71
 aligned with PEX13_YEAST | P80667 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:71
                                   310       320       330       340       350       360       370 
          PEX13_YEAST   301 EPIDPSKLEFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEIIK 371
               SCOP domains d1n5za_ A: Peroxisomal membrane protein Pex13p                          SCOP domains
               CATH domains 1n5zA00 A:7-77 SH3 Domains                                              CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhheeeee...................eeeeeeee.....eeeeeeeee....eeeee...eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SH3  PDB: A:12-77 UniProt: 306-372                                 PROSITE
               Transcript 2 Exon 2.1  PDB: A:7-77 UniProt: 1-386 [INCOMPLETE]                       Transcript 2
                 1n5z A   7 EPIDPSKLEFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEIIK  77
                                    16        26        36        46        56        66        76 


Chain B from PDB  Type:PROTEIN  Length:69
 aligned with PEX13_YEAST | P80667 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:69
                                   314       324       334       344       354       364         
          PEX13_YEAST   305 PSKLEFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEIIKRR 373
               SCOP domains d1n5zb_ B: Peroxisomal membrane protein Pex13p                        SCOP domains
               CATH domains 1n5zB00 B:11-79 SH3 Domains                                           CATH domains
           Pfam domains (1) -------SH3_1-1n5zB01 B:18-70                                --------- Pfam domains (1)
           Pfam domains (2) -------SH3_1-1n5zB02 B:18-70                                --------- Pfam domains (2)
         Sec.struct. author .....eeee...................eeeeeeee.....eeeeeeeee....eeeee...eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SH3  PDB: B:12-78 UniProt: 306-372                                 - PROSITE
               Transcript 2 Exon 2.1  PDB: B:11-79 UniProt: 1-386 [INCOMPLETE]                    Transcript 2
                 1n5z B  11 PSKLEFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEIIKRR  79
                                    20        30        40        50        60        70         


Chain P from PDB  Type:PROTEIN  Length:10
 aligned with PEX14_YEAST | P53112 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:10
                                    94
          PEX14_YEAST    85 MPPTLPHRDW  94
               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 1 Exon 1.1   Transcript 1
                 1n5z P   3 MPPTLPHRDW  12
                                    12


Chain Q from PDB  Type:PROTEIN  Length:10
 aligned with PEX14_YEAST | P53112 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:10
                                    94
          PEX14_YEAST    85 MPPTLPHRDW  94
               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 1 Exon 1.1   Transcript 1
                 1n5z Q   3 MPPTLPHRDW  12
                                    12
   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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: SH3 (175)

(-) Gene Ontology  (11, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

Chain P,Q   (PEX14_YEAST | P53112)
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: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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  1n5z
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  PEX14_YEAST | P53112
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 Related Entries

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

UniProtKB/Swiss-Prot
        PEX13_YEAST | P80667: 1jqq 1nm7 2v1r
        PEX14_YEAST | P53112: 2v1r

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