PDBsum entry 1w70

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Sh3 domain PDB id
Protein chains
60 a.a. *
14 a.a. *
12 a.a. *
SO4 ×4
TFA ×2
Waters ×227
* Residue conservation analysis
PDB id:
Name: Sh3 domain
Title: Sh3 domain of p40phox complexed with c-terminal polyproline region of p47phox
Structure: Neutrophil cytosol factor 4. Chain: a, b. Fragment: sh3 domain, residues 174-228. Synonym: ncf-4, neutrophil NADPH oxidase factor 4, p40phox, p40-phox. Engineered: yes. Neutrophil cytosol factor 1. Chain: c, d. Fragment: polyproline motif, residues 360-372.
Source: Homo sapiens. Human. Organism_taxid: 9606. Cell: neutrophil. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Cell: neutrophil
Biol. unit: Dimer (from PDB file)
1.46Å     R-factor:   0.181     R-free:   0.207
Authors: C.Massenet,S.Chenavas,C.Cohen-Addad,M.-C.Dagher,G.Brandolin, E.Pebay-Peyroula,F.Fieschi
Key ref:
C.Massenet et al. (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. PubMed id: 15657040 DOI: 10.1074/jbc.M412897200
26-Aug-04     Release date:   18-Jan-05    
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Protein chains
Pfam   ArchSchema ?
Q15080  (NCF4_HUMAN) -  Neutrophil cytosol factor 4
339 a.a.
60 a.a.*
Protein chain
Pfam   ArchSchema ?
P14598  (NCF1_HUMAN) -  Neutrophil cytosol factor 1
390 a.a.
13 a.a.
Protein chain
Pfam   ArchSchema ?
P14598  (NCF1_HUMAN) -  Neutrophil cytosol factor 1
390 a.a.
11 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)


DOI no: 10.1074/jbc.M412897200 J Biol Chem 280:13752-13761 (2005)
PubMed id: 15657040  
Effects of p47phox C terminus phosphorylations on binding interactions with p40phox and p67phox. Structural and functional comparison of p40phox and p67phox SH3 domains.
C.Massenet, S.Chenavas, C.Cohen-Addad, M.C.Dagher, G.Brandolin, E.Pebay-Peyroula, F.Fieschi.
The neutrophil NADPH oxidase produces superoxide anions in response to infection. This reaction is activated by association of cytosolic factors, p47phox and p67phox, and a small G protein Rac with the membranous flavocytochrome b558. Another cytosolic factor, p40phox, is associated to the complex and is reported to play regulatory roles. Initiation of the NADPH oxidase activation cascade has been reported as consecutive to phosphorylation on serines 359/370 and 379 of the p47phox C terminus. These serines surround a polyproline motif that can interact with the Src homology 3 (SH3) module of p40phox (SH3p40) or the C-terminal SH3 of p67phox (C-SH3p67). The latter one presents a higher affinity in the resting state for p47phox. A change in SH3 binding preference following phosphorylation has been postulated earlier. Here we report the crystal structures of SH3p40 alone or in complex with a 12-residue proline-rich region of p47phox at 1.46 angstrom resolution. Using intrinsic tryptophan fluorescence measurements, we compared the affinity of the strict polyproline motif and the whole C terminus peptide with both SH3p40 and C-SH3p67. These data reveal that SH3p40 can interact with a consensus polyproline motif but also with a noncanonical motif of the p47phox C terminus. The electrostatic surfaces of both SH3 are very different, and therefore the binding preference for C-SH3p67 can be attributed to the polyproline motif recognition and particularly to the Arg-368p47 binding mode. The noncanonical motif contributes equally to interaction with both SH3. The influence of serine phosphorylation on residues 359/370 and 379 on the affinity for both SH3 domains has been checked. We conclude that contrarily to previous suggestions, phosphorylation of Ser-359/370 does not modify the SH3 binding affinity for both SH3, whereas phosphorylation of Ser-379 has a destabilizing effect on both interactions. Other mechanisms than a phosphorylation induced switch between the two SH3 must therefore take place for NADPH oxidase activation cascade to start.
  Selected figure(s)  
Figure 4.
FIG. 4. Interaction between polyProp47 and SH3^p40. The plot shows the p47^phox polyproline motif (residue Cys (C)) surrounded by interacting residues of SH3^p40 (residue Ala (A)). p40^phox residues at hydrogen bond distances from polyProp47 are indicated (distances in Å), and residues within van der Waals distances are labeled. The figure was drawn with LIGPLOT (59).
Figure 5.
FIG. 5. Interaction interface of the non-PXXP motif of p47^phox-Cter with C-SH3^p67. The surface of C-SH3^p67 is drawn in white and p47^phox-Cter in green. The complex used is the most representative structure from PDB file 1k4u [PDB] (41). Side chain residues of C-SH3^p67 are in yellow. The corresponding residues of SH3^p40 are indicated in parentheses. The figure was drawn with PyMol.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 13752-13761) copyright 2005.  
  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.  
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.  
19593437 A.Deniaud, A.Goulielmakis, J.Covès, and E.Pebay-Peyroula (2009).
Differences between CusA and AcrB crystallisation highlighted by protein flexibility.
  PLoS One, 4, e6214.  
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.  
  20107577 R.Niesner, P.Narang, H.Spiecker, V.Andresen, K.H.Gericke, and M.Gunzer (2008).
Selective detection of NADPH oxidase in polymorphonuclear cells by means of NAD(P)H-based fluorescence lifetime imaging.
  J Biophys, 2008, 602639.  
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.  
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.  
17363896 R.K.Mahadev, S.M.Di Pietro, J.M.Olson, H.L.Piao, G.S.Payne, and M.Overduin (2007).
Structure of Sla1p homology domain 1 and interaction with the NPFxD endocytic internalization motif.
  EMBO J, 26, 1963-1971.
PDB code: 2hbp
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.  
16880255 C.I.Suh, N.D.Stull, X.J.Li, W.Tian, M.O.Price, S.Grinstein, M.B.Yaffe, S.Atkinson, and M.C.Dinauer (2006).
The phosphoinositide-binding protein p40phox activates the NADPH oxidase during FcgammaIIA receptor-induced phagocytosis.
  J Exp Med, 203, 1915-1925.  
  17012801 K.Honbou, S.Yuzawa, N.N.Suzuki, Y.Fujioka, H.Sumimoto, and F.Inagaki (2006).
Crystallization and preliminary crystallographic analysis of p40phox, a regulatory subunit of NADPH oxidase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1018-1020.  
16987008 R.Takeya, and H.Sumimoto (2006).
Regulation of novel superoxide-producing NAD(P)H oxidases.
  Antioxid Redox Signal, 8, 1523-1532.  
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.