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PDBsum entry 1k4u

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protein Protein-protein interface(s) links
Hormone/growth factor PDB id
1k4u
Jmol
Contents
Protein chains
62 a.a. *
32 a.a. *
* Residue conservation analysis
PDB id:
1k4u
Name: Hormone/growth factor
Title: Solution structure of thE C-terminal sh3 domain of p67phox complexed with thE C-terminal tail region of p47phox
Structure: Phagocyte NADPH oxidase subunit p67phox. Chain: s. Fragment: c-terminal sh3 domain (residues 455-516). Synonym: neutrophil cytosol factor 2. Engineered: yes. Mutation: yes. Phagocyte NADPH oxidase subunit p47phox. Chain: p. Fragment: tail peptide (residues 359-390).
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ncf2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: ncf1.
NMR struc: 22 models
Authors: K.Kami,R.Takeya,H.Sumimoto,D.Kohda
Key ref:
K.Kami et al. (2002). Diverse recognition of non-PxxP peptide ligands by the SH3 domains from p67(phox), Grb2 and Pex13p. EMBO J, 21, 4268-4276. PubMed id: 12169629 DOI: 10.1093/emboj/cdf428
Date:
08-Oct-01     Release date:   08-Apr-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P19878  (NCF2_HUMAN) -  Neutrophil cytosol factor 2
Seq:
Struc:
 
Seq:
Struc:
526 a.a.
62 a.a.*
Protein chain
Pfam   ArchSchema ?
P14598  (NCF1_HUMAN) -  Neutrophil cytosol factor 1
Seq:
Struc:
390 a.a.
32 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biochemical function     superoxide-generating NADPH oxidase activity     1 term  

 

 
DOI no: 10.1093/emboj/cdf428 EMBO J 21:4268-4276 (2002)
PubMed id: 12169629  
 
 
Diverse recognition of non-PxxP peptide ligands by the SH3 domains from p67(phox), Grb2 and Pex13p.
K.Kami, R.Takeya, H.Sumimoto, D.Kohda.
 
  ABSTRACT  
 
The basic function of the Src homology 3 (SH3) domain is considered to be binding to proline-rich sequences containing a PxxP motif. Recently, many SH3 domains, including those from Grb2 and Pex13p, were reported to bind sequences lacking a PxxP motif. We report here that the 22 residue peptide lacking a PxxP motif, derived from p47(phox), binds to the C-terminal SH3 domain from p67(phox). We applied the NMR cross-saturation method to locate the interaction sites for the non-PxxP peptides on their cognate SH3 domains from p67(phox), Grb2 and Pex13p. The binding site of the Grb2 SH3 partially overlapped the conventional PxxP-binding site, whereas those of p67(phox) and Pex13p SH3s are located in different surface regions. The non-PxxP peptide from p47(phox) binds to the p67(phox) SH3 more tightly when it extends to the N-terminus to include a typical PxxP motif, which enabled the structure determination of the complex, to reveal that the non-PxxP peptide segment interacted with the p67(phox) SH3 in a compact helix-turn-helix structure (PDB entry 1K4U).
 
  Selected figure(s)  
 
Figure 4.
Figure 4 Summary of the binding sites on three SH3 domains for peptides lacking a PxxP motif. The three SH3 domains from p67^phox, Grb2 and Pexp13p accommodate the cognate non-PxxP peptides with different regions on the molecular surfaces. The SLP-76 peptide-binding site on the Grb2 SH3(C) domain partially overlaps the conventional PxxP motif-binding site.
Figure 5.
Figure 5 Structure of the complex of the p67^phox SH3(C) and the p47^phox tail peptide. (A) Overlay of the 22 NMR structures. The residues used for superimposing the different structures are colored blue (SH3) and red (the tail peptide), and the other residues are in gray. Residue numbers of the p47^phox tail peptide are labeled with a prime ('). (B) Ribbon representation of the lowest energy structure. The -strands of the p67^phox SH3(C) are colored blue: 1, residues 460−463; 2, 483−491; 3, 494−498; 4, 503−506; and the 3[10]-helix is colored green: residues 508−510. The PxxP motif and the two -helices of the p47^phox tail peptide are drawn in red and orange, respectively. Side chains located within the binding interface are shown in pink (SH3) and in yellow (the tail peptide). (C) The same structure viewed from a different angle. The side chains of Leu375', Lys383' and Leu386', colored yellow, fill the space between the two -helices. The positions of the three SH3 loops are shown.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 4268-4276) copyright 2002.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21472810 C.B.McDonald, K.L.Seldeen, B.J.Deegan, V.Bhat, and A.Farooq (2011).
Binding of the cSH3 domain of Grb2 adaptor to two distinct RXXK motifs within Gab1 docker employs differential mechanisms.
  J Mol Recognit, 24, 585-596.  
21629295 G.R.Drummond, S.Selemidis, K.K.Griendling, and C.G.Sobey (2011).
Combating oxidative stress in vascular disease: NADPH oxidases as therapeutic targets.
  Nat Rev Drug Discov, 10, 453-471.  
20637895 D.Shao, A.W.Segal, and L.V.Dekker (2010).
Subcellular localisation of the p40phox component of NADPH oxidase involves direct interactions between the Phox homology domain and F-actin.
  Int J Biochem Cell Biol, 42, 1736-1743.  
20410074 E.León, G.Navarro-Avilés, C.M.Santiveri, C.Flores-Flores, M.Rico, C.González, F.J.Murillo, M.Elías-Arnanz, M.A.Jiménez, and S.Padmanabhan (2010).
A bacterial antirepressor with SH3 domain topology mimics operator DNA in sequestering the repressor DNA recognition helix.
  Nucleic Acids Res, 38, 5226-5241.
PDB code: 2kss
20858292 K.Shameer, L.L.Madan, S.Veeranna, B.Gopal, and R.Sowdhamini (2010).
PeptideMine--a webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes.
  BMC Bioinformatics, 11, 473.  
20520783 N.Tyagi, K.Anamika, and N.Srinivasan (2010).
A framework for classification of prokaryotic protein kinases.
  PLoS One, 5, e10608.  
21098279 O.Aitio, M.Hellman, A.Kazlauskas, D.F.Vingadassalom, J.M.Leong, K.Saksela, and P.Permi (2010).
Recognition of tandem PxxP motifs as a unique Src homology 3-binding mode triggers pathogen-driven actin assembly.
  Proc Natl Acad Sci U S A, 107, 21743-21748.
PDB code: 2kxc
20454568 S.Dutta, and K.Rittinger (2010).
Regulation of NOXO1 activity through reversible interactions with p22 and NOXA1.
  PLoS One, 5, e10478.  
19361414 A.Severin, R.E.Joseph, S.Boyken, D.B.Fulton, and A.H.Andreotti (2009).
Proline isomerization preorganizes the Itk SH2 domain for binding to the Itk SH3 domain.
  J Mol Biol, 387, 726-743.  
19323566 C.B.McDonald, K.L.Seldeen, B.J.Deegan, and A.Farooq (2009).
SH3 domains of Grb2 adaptor bind to PXpsiPXR motifs within the Sos1 nucleotide exchange factor in a discriminate manner.
  Biochemistry, 48, 4074-4085.  
19590096 E.J.Stollar, B.Garcia, P.A.Chong, A.Rath, H.Lin, J.D.Forman-Kay, and A.R.Davidson (2009).
Structural, functional, and bioinformatic studies demonstrate the crucial role of an extended peptide binding site for the SH3 domain of yeast Abp1p.
  J Biol Chem, 284, 26918-26927.
PDB code: 2rpn
19372727 J.El-Benna, P.M.Dang, M.A.Gougerot-Pocidalo, J.C.Marie, and F.Braut-Boucher (2009).
p47phox, the phagocyte NADPH oxidase/NOX2 organizer: structure, phosphorylation and implication in diseases.
  Exp Mol Med, 41, 217-225.  
19633357 P.Fernando, J.S.Sandoz, W.Ding, Y.de Repentigny, S.Brunette, J.F.Kelly, R.Kothary, and L.A.Megeney (2009).
Bin1 SRC homology 3 domain acts as a scaffold for myofiber sarcomere assembly.
  J Biol Chem, 284, 27674-27686.  
19129478 X.J.Li, W.Tian, N.D.Stull, S.Grinstein, S.Atkinson, and M.C.Dinauer (2009).
A fluorescently tagged C-terminal fragment of p47phox detects NADPH oxidase dynamics during phagocytosis.
  Mol Biol Cell, 20, 1520-1532.  
18513324 H.Sumimoto (2008).
Structure, regulation and evolution of Nox-family NADPH oxidases that produce reactive oxygen species.
  FEBS J, 275, 3249-3277.  
18200045 J.Rumpf, B.Simon, N.Jung, T.Maritzen, V.Haucke, M.Sattler, and Y.Groemping (2008).
Structure of the Eps15-stonin2 complex provides a molecular explanation for EH-domain ligand specificity.
  EMBO J, 27, 558-569.
PDB code: 2jxc
18804121 S.Selemidis, C.G.Sobey, K.Wingler, H.H.Schmidt, and G.R.Drummond (2008).
NADPH oxidases in the vasculature: molecular features, roles in disease and pharmacological inhibition.
  Pharmacol Ther, 120, 254-291.  
17290225 K.Honbou, R.Minakami, S.Yuzawa, R.Takeya, N.N.Suzuki, S.Kamakura, H.Sumimoto, and F.Inagaki (2007).
Full-length p40phox structure suggests a basis for regulation mechanism of its membrane binding.
  EMBO J, 26, 1176-1186.
PDB code: 2dyb
17190834 K.Murayama, M.Shirouzu, Y.Kawasaki, M.Kato-Murayama, K.Hanawa-Suetsugu, A.Sakamoto, Y.Katsura, A.Suenaga, M.Toyama, T.Terada, M.Taiji, T.Akiyama, and S.Yokoyama (2007).
Crystal structure of the rac activator, Asef, reveals its autoinhibitory mechanism.
  J Biol Chem, 282, 4238-4242.
PDB code: 2dx1
17352427 M.Morell, A.Espargaró, F.X.Avilés, and S.Ventura (2007).
Detection of transient protein-protein interactions by bimolecular fluorescence complementation: the Abl-SH3 case.
  Proteomics, 7, 1023-1036.  
17289588 P.Sarkar, C.Reichman, T.Saleh, R.B.Birge, and C.G.Kalodimos (2007).
Proline cis-trans isomerization controls autoinhibition of a signaling protein.
  Mol Cell, 25, 413-426.  
17900370 T.Kawahara, and J.D.Lambeth (2007).
Molecular evolution of Phox-related regulatory subunits for NADPH oxidase enzymes.
  BMC Evol Biol, 7, 178.  
17122360 T.Ueyama, T.Tatsuno, T.Kawasaki, S.Tsujibe, Y.Shirai, H.Sumimoto, T.L.Leto, and N.Saito (2007).
A regulated adaptor function of p40phox: distinct p67phox membrane targeting by p40phox and by p47phox.
  Mol Biol Cell, 18, 441-454.  
17437541 V.Anggono, and P.J.Robinson (2007).
Syndapin I and endophilin I bind overlapping proline-rich regions of dynamin I: role in synaptic vesicle endocytosis.
  J Neurochem, 102, 931-943.  
16762923 K.Miyano, N.Ueno, R.Takeya, and H.Sumimoto (2006).
Direct involvement of the small GTPase Rac in activation of the superoxide-producing NADPH oxidase Nox1.
  J Biol Chem, 281, 21857-21868.  
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
16987008 R.Takeya, and H.Sumimoto (2006).
Regulation of novel superoxide-producing NAD(P)H oxidases.
  Antioxid Redox Signal, 8, 1523-1532.  
15657040 C.Massenet, S.Chenavas, C.Cohen-Addad, M.C.Dagher, G.Brandolin, E.Pebay-Peyroula, and F.Fieschi (2005).
Effects of p47phox C terminus phosphorylations on binding interactions with p40phox and p67phox. Structural and functional comparison of p40phox and p67phox SH3 domains.
  J Biol Chem, 280, 13752-13761.
PDB codes: 1w6x 1w70
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.  
16006427 K.Hashimoto, Z.Kato, T.Nagase, N.Shimozawa, K.Kuwata, K.Omoya, A.Li, E.Matsukuma, Y.Yamamoto, H.Ohnishi, H.Tochio, M.Shirakawa, Y.Suzuki, R.J.Wanders, and N.Kondo (2005).
Molecular mechanism of a temperature-sensitive phenotype in peroxisomal biogenesis disorder.
  Pediatr Res, 58, 263-269.  
15824103 N.Ueno, R.Takeya, K.Miyano, H.Kikuchi, and H.Sumimoto (2005).
The NADPH oxidase Nox3 constitutively produces superoxide in a p22phox-dependent manner: its regulation by oxidase organizers and activators.
  J Biol Chem, 280, 23328-23339.  
16025326 Y.Inoue, M.Ogasawara, T.Moroi, M.Satake, K.Azumi, T.Moritomo, and T.Nakanishi (2005).
Characteristics of NADPH oxidase genes (Nox2, p22, p47, and p67) and Nox4 gene expressed in blood cells of juvenile Ciona intestinalis.
  Immunogenetics, 57, 520-534.  
15483625 C.Kojima, A.Hashimoto, I.Yabuta, M.Hirose, S.Hashimoto, Y.Kanaho, H.Sumimoto, T.Ikegami, and H.Sabe (2004).
Regulation of Bin1 SH3 domain binding by phosphoinositides.
  EMBO J, 23, 4413-4422.  
15365846 J.M.Robinson, T.Ohira, and J.A.Badwey (2004).
Regulation of the NADPH-oxidase complex of phagocytic leukocytes. Recent insights from structural biology, molecular genetics, and microscopy.
  Histochem Cell Biol, 122, 293-304.  
15341735 K.Saito, T.Kigawa, S.Koshiba, K.Sato, Y.Matsuo, A.Sakamoto, T.Takagi, M.Shirouzu, T.Yabuki, E.Nunokawa, E.Seki, T.Matsuda, M.Aoki, Y.Miyata, N.Hirakawa, M.Inoue, T.Terada, T.Nagase, R.Kikuno, M.Nakayama, O.Ohara, A.Tanaka, and S.Yokoyama (2004).
The CAP-Gly domain of CYLD associates with the proline-rich sequence in NEMO/IKKgamma.
  Structure, 12, 1719-1728.
PDB code: 1ixd
15100220 M.Lewitzky, M.Harkiolaki, M.C.Domart, E.Y.Jones, and S.M.Feller (2004).
Mona/Gads SH3C binding to hematopoietic progenitor kinase 1 (HPK1) combines an atypical SH3 binding motif, R/KXXK, with a classical PXXP motif embedded in a polyproline type II (PPII) helix.
  J Biol Chem, 279, 28724-28732.
PDB code: 1uti
14978303 M.R.Ferguson, X.Fan, M.Mukherjee, J.Luo, R.Khan, J.C.Ferreon, V.J.Hilser, R.E.Shope, and R.O.Fox (2004).
Directed discovery of bivalent peptide ligands to an SH3 domain.
  Protein Sci, 13, 626-632.  
15293055 W.M.Nauseef (2004).
Assembly of the phagocyte NADPH oxidase.
  Histochem Cell Biol, 122, 277-291.  
12473664 B.Bánfi, R.A.Clark, K.Steger, and K.H.Krause (2003).
Two novel proteins activate superoxide generation by the NADPH oxidase NOX1.
  J Biol Chem, 278, 3510-3513.  
12874286 K.Kowanetz, I.Szymkiewicz, K.Haglund, M.Kowanetz, K.Husnjak, J.D.Taylor, P.Soubeyran, U.Engstrom, J.E.Ladbury, and I.Dikic (2003).
Identification of a novel proline-arginine motif involved in CIN85-dependent clustering of Cbl and down-regulation of epidermal growth factor receptors.
  J Biol Chem, 278, 39735-39746.  
12773374 M.Harkiolaki, M.Lewitzky, R.J.Gilbert, E.Y.Jones, R.P.Bourette, G.Mouchiroud, H.Sondermann, I.Moarefi, and S.M.Feller (2003).
Structural basis for SH3 domain-mediated high-affinity binding between Mona/Gads and SLP-76.
  EMBO J, 22, 2571-2582.
PDB code: 1oeb
12887891 M.I.Wilson, D.J.Gill, O.Perisic, M.T.Quinn, and R.L.Williams (2003).
PB1 domain-mediated heterodimerization in NADPH oxidase and signaling complexes of atypical protein kinase C with Par6 and p62.
  Mol Cell, 12, 39-50.
PDB code: 1oey
12620234 Q.Liu, D.Berry, P.Nash, T.Pawson, C.J.McGlade, and S.S.Li (2003).
Structural basis for specific binding of the Gads SH3 domain to an RxxK motif-containing SLP-76 peptide: a novel mode of peptide recognition.
  Mol Cell, 11, 471-481.
PDB code: 1h3h
12716910 R.Takeya, N.Ueno, K.Kami, M.Taura, M.Kohjima, T.Izaki, H.Nunoi, and H.Sumimoto (2003).
Novel human homologues of p47phox and p67phox participate in activation of superoxide-producing NADPH oxidases.
  J Biol Chem, 278, 25234-25246.  
13129930 T.Kaneko, T.Kumasaka, T.Ganbe, T.Sato, K.Miyazawa, N.Kitamura, and N.Tanaka (2003).
Structural insight into modest binding of a non-PXXP ligand to the signal transducing adaptor molecule-2 Src homology 3 domain.
  J Biol Chem, 278, 48162-48168.
PDB code: 1uj0
14674751 W.Shao, S.C.Im, E.R.Zuiderweg, and L.Waskell (2003).
Mapping the binding interface of the cytochrome b5-cytochrome c complex by nuclear magnetic resonance.
  Biochemistry, 42, 14774-14784.  
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.