PDBsum entry 1nm7

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protein links
Protein transport PDB id
Protein chain
61 a.a. *
* Residue conservation analysis
PDB id:
Name: Protein transport
Title: Solution structure of the scpex13p sh3 domain
Structure: Peroxisomal membrane protein pas20. Chain: a. Fragment: sh3 domain. Synonym: pex13p sh3 domain. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 10 models
Authors: J.R.Pires,X.Hong,C.Brockmann,R.Volkmer-Engert,J.Schneider- Mergener,H.Oschkinat,R.Erdmann
Key ref:
J.R.Pires et al. (2003). The ScPex13p SH3 domain exposes two distinct binding sites for Pex5p and Pex14p. J Mol Biol, 326, 1427-1435. PubMed id: 12595255 DOI: 10.1016/S0022-2836(03)00039-1
09-Jan-03     Release date:   04-Mar-03    
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Protein chain
Pfam   ArchSchema ?
P80667  (PEX13_YEAST) -  Peroxisomal membrane protein PAS20
386 a.a.
61 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1016/S0022-2836(03)00039-1 J Mol Biol 326:1427-1435 (2003)
PubMed id: 12595255  
The ScPex13p SH3 domain exposes two distinct binding sites for Pex5p and Pex14p.
J.R.Pires, X.Hong, C.Brockmann, R.Volkmer-Engert, J.Schneider-Mergener, H.Oschkinat, R.Erdmann.
Pex13p is an essential component of the peroxisomal protein import machinery and interacts via its C-terminal SH3 domain with the type II SH3-ligand Pex14p and the non-PXXP protein Pex5p. We report the solution structure of the SH3 domain of Pex13p from Saccharomyces cerevisiae and the identification of a novel-binding pocket, which binds a non-PXXP-peptide representing the binding site of Pex5p. Chemical shift assays revealed the binding sites for Pex5p and Pex14p ligand peptides to be distinct and spatially separated. Competition assays demonstrated that the two ligand peptides can bind simultaneously to the SH3 domain.
  Selected figure(s)  
Figure 2.
Figure 2. Identification of the SH3-binding fragments of Pex5p and Pex14p. (A) Two hybrid interactions of Pex13p[aa285-386] and various fragments of ScPex5p. Interactions were analyzed by the b-galactosidase filter assay. (B) Cellulose membranes decorated with 26-mer peptides covering amino acid residues 181-312 of ScPex5p with one-amino acid shifts between neighboring peptides and (C) 12-mer peptides covering the entire protein sequence of ScPex14p with three-amino acid shifts between neighboring peptides were incubated with the recombinant GST-tagged SH3 domain of ScPex13p. Peptide-SH3complexes were identified by the peptide spot overlay assay using antibodies against GST.
Figure 6.
Figure 6. ScPex13p SH3 domain-binding sites for Pex5p and Pex14p. Domain surface and ribbon representation. Only residues showing strong chemical shift changes upon addition of Pex14p (red) and Pex5p (blue) are colored.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 326, 1427-1435) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20454568 S.Dutta, and K.Rittinger (2010).
Regulation of NOXO1 activity through reversible interactions with p22 and NOXA1.
  PLoS One, 5, e10478.  
20146669 T.Lanyon-Hogg, S.L.Warriner, and A.Baker (2010).
Getting a camel through the eye of a needle: the import of folded proteins by peroxisomes.
  Biol Cell, 102, 245-263.  
19656396 J.Vyas, R.J.Nowling, M.W.Maciejewski, S.Rajasekaran, M.R.Gryk, and M.R.Schiller (2009).
A proposed syntax for Minimotif Semantics, version 1.
  BMC Genomics, 10, 360.  
19841731 R.Tonikian, X.Xin, C.P.Toret, D.Gfeller, C.Landgraf, S.Panni, S.Paoluzi, L.Castagnoli, B.Currell, S.Seshagiri, H.Yu, B.Winsor, M.Vidal, M.B.Gerstein, G.D.Bader, R.Volkmer, G.Cesareni, D.G.Drubin, P.M.Kim, S.S.Sidhu, and C.Boone (2009).
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins.
  PLoS Biol, 7, e1000218.  
19437530 R.Volkmer (2009).
Synthesis and application of peptide arrays: quo vadis SPOT technology.
  Chembiochem, 10, 1431-1442.  
16766517 K.Ma, J.G.Forbes, G.Gutierrez-Cruz, and K.Wang (2006).
Titin as a giant scaffold for integrating stress and Src homology domain 3-mediated signaling pathways: the clustering of novel overlap ligand motifs in the elastic PEVK segment.
  J Biol Chem, 281, 27539-27556.  
16644733 M.R.Schiller, K.Chakrabarti, G.F.King, N.I.Schiller, B.A.Eipper, and M.W.Maciejewski (2006).
Regulation of RhoGEF activity by intramolecular and intermolecular SH3 domain interactions.
  J Biol Chem, 281, 18774-18786.
PDB code: 1u3o
15798189 A.Schell-Steven, K.Stein, M.Amoros, C.Landgraf, R.Volkmer-Engert, H.Rottensteiner, and R.Erdmann (2005).
Identification of a novel, intraperoxisomal pex14-binding site in pex13: association of pex13 with the docking complex is essential for peroxisomal matrix protein import.
  Mol Cell Biol, 25, 3007-3018.  
15723349 A.le Maire, T.Weber, S.Saunier, I.Broutin, C.Antignac, A.Ducruix, and F.Dardel (2005).
Solution NMR structure of the SH3 domain of human nephrocystin and analysis of a mutation-causing juvenile nephronophthisis.
  Proteins, 59, 347-355.
PDB code: 1s1n
16158059 C.Reichman, K.Singh, Y.Liu, S.Singh, H.Li, J.E.Fajardo, A.Fiser, and R.B.Birge (2005).
Transactivation of Abl by the Crk II adapter protein requires a PNAY sequence in the Crk C-terminal SH3 domain.
  Oncogene, 24, 8187-8199.  
15885087 I.Heiland, and R.Erdmann (2005).
Biogenesis of peroxisomes. Topogenesis of the peroxisomal membrane and matrix proteins.
  FEBS J, 272, 2362-2372.  
15679822 R.J.Wanders, and H.R.Waterham (2005).
Peroxisomal disorders I: biochemistry and genetics of peroxisome biogenesis disorders.
  Clin Genet, 67, 107-133.  
15539076 J.Moyersoen, J.Choe, E.Fan, W.G.Hol, and P.A.Michels (2004).
Biogenesis of peroxisomes and glycosomes: trypanosomatid glycosome assembly is a promising new drug target.
  FEMS Microbiol Rev, 28, 603-643.  
15146459 N.Shimozawa, T.Tsukamoto, T.Nagase, Y.Takemoto, N.Koyama, Y.Suzuki, M.Komori, T.Osumi, G.Jeannette, R.J.Wanders, and N.Kondo (2004).
Identification of a new complementation group of the peroxisome biogenesis disorders and PEX14 as the mutated gene.
  Hum Mutat, 23, 552-558.  
14754507 L.A.Brown, and A.Baker (2003).
Peroxisome biogenesis and the role of protein import.
  J Cell Mol Med, 7, 388-400.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.