PDBsum entry 2dyb

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protein Protein-protein interface(s) links
Oxidoreductase PDB id
Protein chains
298 a.a. *
273 a.a. *
* Residue conservation analysis
PDB id:
Name: Oxidoreductase
Title: The crystal structure of human p40(phox)
Structure: Neutrophil cytosol factor 4. Chain: a, b. Synonym: ncf-4, neutrophil NADPH oxidase factor 4, p40- phox, p40phox. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
3.15Å     R-factor:   0.263     R-free:   0.302
Authors: K.Honbou
Key ref:
K.Honbou et al. (2007). Full-length p40phox structure suggests a basis for regulation mechanism of its membrane binding. EMBO J, 26, 1176-1186. PubMed id: 17290225 DOI: 10.1038/sj.emboj.7601561
08-Sep-06     Release date:   23-Jan-07    
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Protein chain
Pfam   ArchSchema ?
Q15080  (NCF4_HUMAN) -  Neutrophil cytosol factor 4
339 a.a.
298 a.a.*
Protein chain
Pfam   ArchSchema ?
Q15080  (NCF4_HUMAN) -  Neutrophil cytosol factor 4
339 a.a.
273 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     membrane   7 terms 
  Biological process     phagosome maturation   8 terms 
  Biochemical function     protein binding     6 terms  


DOI no: 10.1038/sj.emboj.7601561 EMBO J 26:1176-1186 (2007)
PubMed id: 17290225  
Full-length p40phox structure suggests a basis for regulation mechanism of its membrane binding.
K.Honbou, R.Minakami, S.Yuzawa, R.Takeya, N.N.Suzuki, S.Kamakura, H.Sumimoto, F.Inagaki.
The superoxide-producing phagocyte NADPH oxidase is activated during phagocytosis to destroy ingested microbes. The adaptor protein p40phox associates via the PB1 domain with the essential oxidase activator p67phox, and is considered to function by recruiting p67phox to phagosomes; in this process, the PX domain of p40phox binds to phosphatidylinositol 3-phosphate [PtdIns(3)P], a lipid abundant in the phagosomal membrane. Here we show that the PtdIns(3)P-binding activity of p40phox is normally inhibited by the PB1 domain both in vivo and in vitro. The crystal structure of the full-length p40phox reveals that the inhibition is mediated via intramolecular interaction between the PB1 and PX domains. The interface of the p40phox PB1 domain for the PX domain localizes on the opposite side of that for the p67phox PB1 domain, and thus the PB1-mediated PX regulation occurs without preventing the PB1-PB1 association with p67phox.
  Selected figure(s)  
Figure 3.
Figure 3 The interface between the PX domain and the PB1 domain. (A) A ribbon diagram of Molecule A. Each domain of p40^phox is colored coded as in Figure 1A. (B) Stereo diagram of a close-up view (the region corresponds to the rectangle in (A)) of the interface between the PX domain and the PB1 domain. Amino-acid residues involved in the interaction are shown in a stick representation. (C) Superposition of the p40^phox PX domain complexed with PtdIns(3)P (blue; PDB code 1H6H) onto that of crystal structure of p40^phox (yellow). The SH3 domain is removed for clarity. PtdIns(3)P, R58, R60, and R105 of the each PX domain, and E259 and D269 of the PB1 domain, which interact with R58 and R60 respectively, are shown in a stick representation. (D) The model of the interaction between the full-length p40^phox and membrane-bound PtdIns(3)P. SH3 domain is connected by dashed line, since relative position of the SH3 domain does not seem to be restricted.
Figure 5.
Figure 5 Dual roles for the PB1 domain of p40^phox. (A) Ribbon diagram of the superposition of p40^phox/p67^phox PB1 heterodimer (blue is p67^phox PB1 and orange is p40^phox PB1; PDB code 1OEY) onto that of the full-length p40^phox (color coded as in Figure 1A). A C-terminal extension region is shown in dashed circle. (B) Subcellular distribution of GFP-tagged p40^phox and HA-tagged p67^phox in transiently transfected HeLa cells. Left panel, distribution of GFP-tagged p40^phox in fixed HeLa cells (green); right panel, distribution of endogenous HA-tagged p67^phox (red) and Hoechst staining of the nucleus (blue) in the same field of fixed HeLa cells. The insets show the magnified views. Scale bar, 5 m. (C) Proteins of lysates prepared from HeLa cells expressing both p40^phox and p67^phox were immunoprecipitated (IP) with the anti-GFP or control IgG, and then analyzed by immunoblot (Blot) with the anti-HA or anti-GFP antibodies. (D) In vitro interaction between purified GST-p40^phox and His-tagged p67^phox in the presence or absence of PtdIns(3)P.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2007, 26, 1176-1186) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20842512 B.Yu, Y.Chen, Q.Wu, P.Li, Y.Shao, J.Zhang, Q.Zhong, X.Peng, H.Yang, X.Hu, B.Chen, M.Guan, J.Wan, and W.Zhang (2011).
The association between single-nucleotide polymorphisms of NCF2 and systemic lupus erythematosus in Chinese mainland population.
  Clin Rheumatol, 30, 521-527.  
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.  
20336680 F.Susta, D.Chiasserini, K.Fettucciari, P.L.Orvietani, F.Quotadamo, R.Noce, A.Bartoli, P.Marconi, L.Corazzi, and L.Binaglia (2010).
Protein expression changes induced in murine peritoneal macrophages by Group B Streptococcus.
  Proteomics, 10, 2099-2112.  
20803017 G.Y.Lam, J.Huang, and J.H.Brumell (2010).
The many roles of NOX2 NADPH oxidase-derived ROS in immunity.
  Semin Immunopathol, 32, 415-430.  
20861461 T.A.Chessa, K.E.Anderson, Y.Hu, Q.Xu, O.Rausch, L.R.Stephens, and P.T.Hawkins (2010).
Phosphorylation of threonine 154 in p40phox is an important physiological signal for activation of the neutrophil NADPH oxidase.
  Blood, 116, 6027-6036.  
20559318 T.G.Kutateladze (2010).
Translation of the phosphoinositide code by PI effectors.
  Nat Chem Biol, 6, 507-513.  
19257809 G.Muller, and H.Morawietz (2009).
Nitric oxide, NAD(P)H oxidase, and atherosclerosis.
  Antioxid Redox Signal, 11, 1711-1731.  
19534724 K.Miyano, H.Koga, R.Minakami, and H.Sumimoto (2009).
The insert region of the Rac GTPases is dispensable for activation of superoxide-producing NADPH oxidases.
  Biochem J, 422, 373-382.  
19438290 T.L.Leto, S.Morand, D.Hurt, and T.Ueyama (2009).
Targeting and regulation of reactive oxygen species generation by Nox family NADPH oxidases.
  Antioxid Redox Signal, 11, 2607-2619.  
18513324 H.Sumimoto (2008).
Structure, regulation and evolution of Nox-family NADPH oxidases that produce reactive oxygen species.
  FEBS J, 275, 3249-3277.  
18755982 K.E.Anderson, K.B.Boyle, K.Davidson, T.A.Chessa, S.Kulkarni, G.E.Jarvis, A.Sindrilaru, K.Scharffetter-Kochanek, O.Rausch, L.R.Stephens, and P.T.Hawkins (2008).
CD18-dependent activation of the neutrophil NADPH oxidase during phagocytosis of Escherichia coli or Staphylococcus aureus is regulated by class III but not class I or II PI3Ks.
  Blood, 112, 5202-5211.  
18211830 R.Ginnan, B.J.Guikema, K.E.Halligan, H.A.Singer, and D.Jourd'heuil (2008).
Regulation of smooth muscle by inducible nitric oxide synthase and NADPH oxidase in vascular proliferative diseases.
  Free Radic Biol Med, 44, 1232-1245.  
18029359 S.A.Bissonnette, C.M.Glazier, M.Q.Stewart, G.E.Brown, C.D.Ellson, and M.B.Yaffe (2008).
Phosphatidylinositol 3-Phosphate-dependent and -independent Functions of p40phox in Activation of the Neutrophil NADPH Oxidase.
  J Biol Chem, 283, 2108-2119.  
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.  
18711001 W.Tian, X.J.Li, N.D.Stull, W.Ming, C.I.Suh, S.A.Bissonnette, M.B.Yaffe, S.Grinstein, S.J.Atkinson, and M.C.Dinauer (2008).
Fc{gamma}R-stimulated activation of the NADPH oxidase: phosphoinositide-binding protein p40phox regulates NADPH oxidase activity after enzyme assembly on the phagosome.
  Blood, 112, 3867-3877.  
17698849 J.Chen, R.He, R.D.Minshall, M.C.Dinauer, and R.D.Ye (2007).
Characterization of a mutation in the Phox homology domain of the NADPH oxidase component p40phox identifies a mechanism for negative regulation of superoxide production.
  J Biol Chem, 282, 30273-30284.  
17707914 T.G.Kutateladze (2007).
Mechanistic similarities in docking of the FYVE and PX domains to phosphatidylinositol 3-phosphate containing membranes.
  Prog Lipid Res, 46, 315-327.  
17900370 T.Kawahara, and J.D.Lambeth (2007).
Molecular evolution of Phox-related regulatory subunits for NADPH oxidase enzymes.
  BMC Evol Biol, 7, 178.  
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.