1k4u: Difference between revisions

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{{Seed}}
[[Image:1k4u.png|left|200px]]


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==Solution structure of the C-terminal SH3 domain of p67phox complexed with the C-terminal tail region of p47phox==
The line below this paragraph, containing "STRUCTURE_1k4u", creates the "Structure Box" on the page.
<StructureSection load='1k4u' size='340' side='right'caption='[[1k4u]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1k4u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K4U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K4U FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1k4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k4u OCA], [https://pdbe.org/1k4u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k4u RCSB], [https://www.ebi.ac.uk/pdbsum/1k4u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k4u ProSAT]</span></td></tr>
{{STRUCTURE_1k4u|  PDB=1k4u  |  SCENE=  }}
</table>
== Disease ==
[https://www.uniprot.org/uniprot/NCF2_HUMAN NCF2_HUMAN] Defects in NCF2 are a cause of chronic granulomatous disease autosomal recessive cytochrome-b-positive type 2 (CGD2) [MIM:[https://omim.org/entry/233710 233710]. Chronic granulomatous disease is a genetically heterogeneous disorder characterized by the inability of neutrophils and phagocytes to kill microbes that they have ingested. Patients suffer from life-threatening bacterial/fungal infections.<ref>PMID:8286749</ref> <ref>PMID:9070911</ref> <ref>PMID:10498624</ref> <ref>PMID:10598813</ref> <ref>PMID:11112388</ref> <ref>PMID:16937026</ref> <ref>PMID:18625437</ref> <ref>PMID:19624736</ref> <ref>PMID:20167518</ref>
== Function ==
[https://www.uniprot.org/uniprot/NCF2_HUMAN NCF2_HUMAN] NCF2, NCF1, and a membrane bound cytochrome b558 are required for activation of the latent NADPH oxidase (necessary for superoxide production).
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k4/1k4u_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1k4u ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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).


===Solution structure of the C-terminal SH3 domain of p67phox complexed with the C-terminal tail region of p47phox===
Diverse recognition of non-PxxP peptide ligands by the SH3 domains from p67(phox), Grb2 and Pex13p.,Kami K, Takeya R, Sumimoto H, Kohda D EMBO J. 2002 Aug 15;21(16):4268-76. PMID:12169629<ref>PMID:12169629</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1k4u" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_12169629}}, adds the Publication Abstract to the page
*[[NADPH oxidase 3D structures|NADPH oxidase 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 12169629 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_12169629}}
__TOC__
 
</StructureSection>
==Disease==
Known disease associated with this structure: Chronic granulomatous disease due to deficiency of NCF-2 OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=608515 608515]], Chronic granulomatous disease due to deficiency of NCF-1 OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=608512 608512]]
 
==About this Structure==
1K4U is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K4U OCA].
 
==Reference==
Diverse recognition of non-PxxP peptide ligands by the SH3 domains from p67(phox), Grb2 and Pex13p., Kami K, Takeya R, Sumimoto H, Kohda D, EMBO J. 2002 Aug 15;21(16):4268-76. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12169629 12169629]
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Kami, K.]]
[[Category: Kami K]]
[[Category: Kohda, D.]]
[[Category: Kohda D]]
[[Category: Sumimoto, H.]]
[[Category: Sumimoto H]]
[[Category: Takeya, R.]]
[[Category: Takeya R]]
[[Category: Helix-turn-helix]]
[[Category: P47phox]]
[[Category: P67phox]]
[[Category: Sh3-peptide complex]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  2 09:46:42 2008''

Latest revision as of 21:12, 29 May 2024

Solution structure of the C-terminal SH3 domain of p67phox complexed with the C-terminal tail region of p47phoxSolution structure of the C-terminal SH3 domain of p67phox complexed with the C-terminal tail region of p47phox

Structural highlights

1k4u is a 2 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

NCF2_HUMAN Defects in NCF2 are a cause of chronic granulomatous disease autosomal recessive cytochrome-b-positive type 2 (CGD2) [MIM:233710. Chronic granulomatous disease is a genetically heterogeneous disorder characterized by the inability of neutrophils and phagocytes to kill microbes that they have ingested. Patients suffer from life-threatening bacterial/fungal infections.[1] [2] [3] [4] [5] [6] [7] [8] [9]

Function

NCF2_HUMAN NCF2, NCF1, and a membrane bound cytochrome b558 are required for activation of the latent NADPH oxidase (necessary for superoxide production).

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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).

Diverse recognition of non-PxxP peptide ligands by the SH3 domains from p67(phox), Grb2 and Pex13p.,Kami K, Takeya R, Sumimoto H, Kohda D EMBO J. 2002 Aug 15;21(16):4268-76. PMID:12169629[10]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ de Boer M, Hilarius-Stokman PM, Hossle JP, Verhoeven AJ, Graf N, Kenney RT, Seger R, Roos D. Autosomal recessive chronic granulomatous disease with absence of the 67-kD cytosolic NADPH oxidase component: identification of mutation and detection of carriers. Blood. 1994 Jan 15;83(2):531-6. PMID:8286749
  2. ↑ Bonizzato A, Russo MP, Donini M, Dusi S. Identification of a double mutation (D160V-K161E) in the p67phox gene of a chronic granulomatous disease patient. Biochem Biophys Res Commun. 1997 Feb 24;231(3):861-3. PMID:9070911 doi:S0006-291X(97)96204-5
  3. ↑ Patino PJ, Rae J, Noack D, Erickson R, Ding J, de Olarte DG, Curnutte JT. Molecular characterization of autosomal recessive chronic granulomatous disease caused by a defect of the nicotinamide adenine dinucleotide phosphate (reduced form) oxidase component p67-phox. Blood. 1999 Oct 1;94(7):2505-14. PMID:10498624
  4. ↑ Noack D, Rae J, Cross AR, Munoz J, Salmen S, Mendoza JA, Rossi N, Curnutte JT, Heyworth PG. Autosomal recessive chronic granulomatous disease caused by novel mutations in NCF-2, the gene encoding the p67-phox component of phagocyte NADPH oxidase. Hum Genet. 1999 Nov;105(5):460-7. PMID:10598813
  5. ↑ Cross AR, Noack D, Rae J, Curnutte JT, Heyworth PG. Hematologically important mutations: the autosomal recessive forms of chronic granulomatous disease (first update). Blood Cells Mol Dis. 2000 Oct;26(5):561-5. PMID:11112388 doi:10.1006/bcmd.2000.0333
  6. ↑ El Kares R, Barbouche MR, Elloumi-Zghal H, Bejaoui M, Chemli J, Mellouli F, Tebib N, Abdelmoula MS, Boukthir S, Fitouri Z, M'Rad S, Bouslama K, Touiri H, Abdelhak S, Dellagi MK. Genetic and mutational heterogeneity of autosomal recessive chronic granulomatous disease in Tunisia. J Hum Genet. 2006;51(10):887-95. Epub 2006 Aug 26. PMID:16937026 doi:10.1007/s10038-006-0039-8
  7. ↑ Yu G, Hong DK, Dionis KY, Rae J, Heyworth PG, Curnutte JT, Lewis DB. Focus on FOCIS: the continuing diagnostic challenge of autosomal recessive chronic granulomatous disease. Clin Immunol. 2008 Aug;128(2):117-26. doi: 10.1016/j.clim.2008.05.008. PMID:18625437 doi:10.1016/j.clim.2008.05.008
  8. ↑ Koker MY, Sanal O, van Leeuwen K, de Boer M, Metin A, Patiroglu T, Ozgur TT, Tezcan I, Roos D. Four different NCF2 mutations in six families from Turkey and an overview of NCF2 gene mutations. Eur J Clin Invest. 2009 Oct;39(10):942-51. doi: 10.1111/j.1365-2362.2009.02195.x., Epub 2009 Jul 17. PMID:19624736 doi:10.1111/j.1365-2362.2009.02195.x
  9. ↑ Roos D, Kuhns DB, Maddalena A, Bustamante J, Kannengiesser C, de Boer M, van Leeuwen K, Koker MY, Wolach B, Roesler J, Malech HL, Holland SM, Gallin JI, Stasia MJ. Hematologically important mutations: the autosomal recessive forms of chronic granulomatous disease (second update). Blood Cells Mol Dis. 2010 Apr 15;44(4):291-9. doi: 10.1016/j.bcmd.2010.01.009., Epub 2010 Feb 18. PMID:20167518 doi:10.1016/j.bcmd.2010.01.009
  10. ↑ Kami K, Takeya R, Sumimoto H, Kohda D. Diverse recognition of non-PxxP peptide ligands by the SH3 domains from p67(phox), Grb2 and Pex13p. EMBO J. 2002 Aug 15;21(16):4268-76. PMID:12169629
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