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(-) Description

Title :  YEAST PEX13 SH3 DOMAIN COMPLEXED WITH A PEPTIDE FROM PEX14 AT 2.1 A RESOLUTION
 
Authors :  I. Kursula, P. Kursula, F. Lehmann, P. Zou, Y. H. Song, M. Wilmanns
Date :  29 May 07  (Deposition) - 03 Jun 08  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,P,Q,R
Biol. Unit 1:  A,Q,R  (1x)
Biol. Unit 2:  B,P  (1x)
Keywords :  Protein Transport, Translocation, Transmembrane, Peptide Complex, Structural Genomics, Peroxisome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Kursula, I. Kursula, N. Pinotsis, F. Lehmann, P. Zou, Y. H. Song, M. Wilmanns
Structural Genomics Of Yeast Sh3 Domains
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEROXISOMAL MEMBRANE PROTEIN PAS20
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PMALC2
    Expression System Vector Type: PLASMID
    Fragment: SH3 DOMAIN, RESIDUES 299-374
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: PEROXIN-13, PEX13
 
Molecule 2 - PEX14
    Chains: P, Q, R
    Engineered: YES
    Fragment: SH3 DOMAIN BINDING SEGMENT, RESIDUES 83-96
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABPQR
Biological Unit 1 (1x): A  QR
Biological Unit 2 (1x):  BP  

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP

(-) Sites  (0, 0)

(no "Site" information available for 2V1R)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V1R)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Met R:3 -Pro R:4

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V1R)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.PEX13_YEAST306-372
 		  2A:12-76
B:12-77
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.PEX13_YEAST306-372
 		  1A:12-76
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.PEX13_YEAST306-372
 		  1-
B:12-77

(-) Exons   (2, 5)

Asymmetric Unit (2, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGL153W1YGL153W.1VII:216278-2173031026PEX14_YEAST1-3413413P:2-10
Q:2-10
R:3-7		9
9
5
2.1YLR191W1YLR191W.1XII:537274-5384341161PEX13_YEAST1-3863862A:10-76
B:10-77		67
68

(-) 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:67
 aligned with PEX13_YEAST | P80667 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:67
                                   313       323       333       343       353       363       
          PEX13_YEAST   304 DPSKLEFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEII 370
               SCOP domains d2v1ra_ A: automated matches                                        SCOP domains
               CATH domains 2v1rA00 A:10-76 SH3 Domains                                         CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhheeeee...................eeeeeeee.....eeeeeeee.....eeeee...eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --SH3  PDB: A:12-76 UniProt: 306-372                                PROSITE
               Transcript 2 Exon 2.1  PDB: A:10-76 UniProt: 1-386 [INCOMPLETE]                  Transcript 2
                 2v1r A  10 DPSKLEFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEII  76
                                    19        29        39        49        59        69       


Chain B from PDB  Type:PROTEIN  Length:68
 aligned with PEX13_YEAST | P80667 from UniProtKB/Swiss-Prot  Length:386

    Alignment length:68
                                   313       323       333       343       353       363        
          PEX13_YEAST   304 DPSKLEFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEIIK 371
               SCOP domains d2v1rb_ B: automated matches                                         SCOP domains
               CATH domains 2v1rB00 B:10-77 SH3 Domains                                          CATH domains
           Pfam domains (1) --------SH3_1-2v1rB01 B:18-70                                ------- Pfam domains (1)
           Pfam domains (2) --------SH3_1-2v1rB02 B:18-70                                ------- Pfam domains (2)
         Sec.struct. author hhhhheeeee...................eeeeeeee.....eeeeeeee.....eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --SH3  PDB: B:12-77 UniProt: 306-372                                 PROSITE
               Transcript 2 Exon 2.1  PDB: B:10-77 UniProt: 1-386 [INCOMPLETE]                   Transcript 2
                 2v1r B  10 DPSKLEFARALYDFVPENPEMEVALKKGDLMAILSKKDPLGRDSDWWKVRTKNGNIGYIPYNYIEIIK  77
                                    19        29        39        49        59        69        


Chain P from PDB  Type:PROTEIN  Length:9
 aligned with PEX14_YEAST | P53112 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:9
          PEX14_YEAST    82 YEAMPPTLP  90
               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
                 2v1r P   2 xEAMPPTLP  10
                            |        
                            2-ACE    


Chain Q from PDB  Type:PROTEIN  Length:9
 aligned with PEX14_YEAST | P53112 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:9
          PEX14_YEAST    82 YEAMPPTLP  90
               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
                 2v1r Q   2 xEAMPPTLP  10
                            |        
                            2-ACE    


Chain R from PDB  Type:PROTEIN  Length:5
 aligned with PEX14_YEAST | P53112 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:5
          PEX14_YEAST    85 MPPTL  89
               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 1.1   Transcript 1
                 2v1r R   3 MPPTL   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, 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,R   (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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  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 1n5z 1nm7
        PEX14_YEAST | P53112: 1n5z

(-) Related Entries Specified in the PDB File

1jqq CRYSTAL STRUCTURE OF PEX13P(301-386) SH3 DOMAIN
1n5z COMPLEX STRUCTURE OF PEX13P SH3 DOMAIN WITH A PEPTIDE OFPEX14P
1nm7 SOLUTION STRUCTURE OF THE SCPEX13P SH3 DOMAIN