1ji4: Difference between revisions

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<StructureSection load='1ji4' size='340' side='right'caption='[[1ji4]], [[Resolution|resolution]] 2.52&Aring;' scene=''>
<StructureSection load='1ji4' size='340' side='right'caption='[[1ji4]], [[Resolution|resolution]] 2.52&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1ji4]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43504 Atcc 43504]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JI4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1JI4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1ji4]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JI4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JI4 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.52&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dps|1dps]], [[1qgh|1qgh]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NAPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 ATCC 43504])</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ji4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji4 OCA], [https://pdbe.org/1ji4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ji4 RCSB], [https://www.ebi.ac.uk/pdbsum/1ji4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ji4 ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1ji4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ji4 OCA], [http://pdbe.org/1ji4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ji4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ji4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ji4 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/DPS_HELPY DPS_HELPY]] Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction (By similarity). Required for the survival in the presence of oxidative stress. Dps is also a virulence factor that activates neutrophils, mast cells and monocytes. It binds to neutrophil-glycosphingolipids and to sulfated carbohydrates on mucin. It might have a role in the accumulation of neutrophils and monocytes at the site of infection. Induces superoxide anion generation, adhesion and chemotaxis of neutrophils, through a pertussis toxin-sensitive pathway involving MAP kinases.<ref>PMID:11069248</ref> <ref>PMID:7768601</ref> <ref>PMID:10790422</ref> <ref>PMID:11857341</ref> <ref>PMID:12672049</ref> <ref>PMID:12748264</ref>
[https://www.uniprot.org/uniprot/DPS_HELPY DPS_HELPY] Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction (By similarity). Required for the survival in the presence of oxidative stress. Dps is also a virulence factor that activates neutrophils, mast cells and monocytes. It binds to neutrophil-glycosphingolipids and to sulfated carbohydrates on mucin. It might have a role in the accumulation of neutrophils and monocytes at the site of infection. Induces superoxide anion generation, adhesion and chemotaxis of neutrophils, through a pertussis toxin-sensitive pathway involving MAP kinases.<ref>PMID:11069248</ref> <ref>PMID:7768601</ref> <ref>PMID:10790422</ref> <ref>PMID:11857341</ref> <ref>PMID:12672049</ref> <ref>PMID:12748264</ref>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Atcc 43504]]
[[Category: Helicobacter pylori]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Battistutta, R]]
[[Category: Battistutta R]]
[[Category: Dundon, W G]]
[[Category: Del Giudice G]]
[[Category: Giudice, G Del]]
[[Category: Dundon WG]]
[[Category: Montecucco, C]]
[[Category: Montecucco C]]
[[Category: Papinutto, E]]
[[Category: Papinutto E]]
[[Category: Rappuoli, R]]
[[Category: Rappuoli R]]
[[Category: Seveso, M]]
[[Category: Seveso M]]
[[Category: Zanotti, G]]
[[Category: Zanotti G]]
[[Category: Dodecamer]]
[[Category: Four-helix bundle]]
[[Category: Metal transport]]

Latest revision as of 11:41, 16 August 2023

NAP protein from helicobacter pyloriNAP protein from helicobacter pylori

Structural highlights

1ji4 is a 12 chain structure with sequence from Helicobacter pylori. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.52Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPS_HELPY Protects DNA from oxidative damage by sequestering intracellular Fe(2+) ion and storing it in the form of Fe(3+) oxyhydroxide mineral. One hydrogen peroxide oxidizes two Fe(2+) ions, which prevents hydroxyl radical production by the Fenton reaction (By similarity). Required for the survival in the presence of oxidative stress. Dps is also a virulence factor that activates neutrophils, mast cells and monocytes. It binds to neutrophil-glycosphingolipids and to sulfated carbohydrates on mucin. It might have a role in the accumulation of neutrophils and monocytes at the site of infection. Induces superoxide anion generation, adhesion and chemotaxis of neutrophils, through a pertussis toxin-sensitive pathway involving MAP kinases.[1] [2] [3] [4] [5] [6]

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

Helicobacter pylori is a major human pathogen associated with severe gastroduodenal diseases, including ulcers and cancers. An H.pylori protein that is highly immunogenic in humans and mice has been identified recently. This protein has been termed HP-NAP, due to its ability of activating neutrophils. In order to achieve a molecular understanding of its unique immunogenic and pro-inflammatory properties, we have determined its three-dimensional structure. Its quaternary structure is similar to that of the dodecameric bacterial ferritins (Dps-like family), but it has a different surface potential charge distribution. This is due to the presence of a large number of positively charged residues, which could well account for its unique ability in activating human leukocytes.

Structure of the neutrophil-activating protein from Helicobacter pylori.,Zanotti G, Papinutto E, Dundon W, Battistutta R, Seveso M, Giudice G, Rappuoli R, Montecucco C J Mol Biol. 2002 Oct 11;323(1):125-30. PMID:12368104[7]

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

See Also

References

  1. ↑ Leakey A, La Brooy J, Hirst R. The ability of Helicobacter pylori to activate neutrophils is determined by factors other than H. pylori neutrophil-activating protein. J Infect Dis. 2000 Dec;182(6):1749-55. Epub 2000 Oct 26. PMID:11069248 doi:http://dx.doi.org/JID000555
  2. ↑ Evans DJ Jr, Evans DG, Takemura T, Nakano H, Lampert HC, Graham DY, Granger DN, Kvietys PR. Characterization of a Helicobacter pylori neutrophil-activating protein. Infect Immun. 1995 Jun;63(6):2213-20. PMID:7768601
  3. ↑ Satin B, Del Giudice G, Della Bianca V, Dusi S, Laudanna C, Tonello F, Kelleher D, Rappuoli R, Montecucco C, Rossi F. The neutrophil-activating protein (HP-NAP) of Helicobacter pylori is a protective antigen and a major virulence factor. J Exp Med. 2000 May 1;191(9):1467-76. PMID:10790422
  4. ↑ Montemurro P, Nishioka H, Dundon WG, de Bernard M, Del Giudice G, Rappuoli R, Montecucco C. The neutrophil-activating protein (HP-NAP) of Helicobacter pylori is a potent stimulant of mast cells. Eur J Immunol. 2002 Mar;32(3):671-6. PMID:11857341 doi:http://dx.doi.org/10.1002/1521-4141(200203)32:3<671::AID-IMMU671>3.0.CO;2-5
  5. ↑ Nishioka H, Baesso I, Semenzato G, Trentin L, Rappuoli R, Del Giudice G, Montecucco C. The neutrophil-activating protein of Helicobacter pylori (HP-NAP) activates the MAPK pathway in human neutrophils. Eur J Immunol. 2003 Apr;33(4):840-9. PMID:12672049 doi:http://dx.doi.org/10.1002/eji.200323726
  6. ↑ Cooksley C, Jenks PJ, Green A, Cockayne A, Logan RP, Hardie KR. NapA protects Helicobacter pylori from oxidative stress damage, and its production is influenced by the ferric uptake regulator. J Med Microbiol. 2003 Jun;52(Pt 6):461-9. PMID:12748264
  7. ↑ Zanotti G, Papinutto E, Dundon W, Battistutta R, Seveso M, Giudice G, Rappuoli R, Montecucco C. Structure of the neutrophil-activating protein from Helicobacter pylori. J Mol Biol. 2002 Oct 11;323(1):125-30. PMID:12368104

1ji4, resolution 2.52Å

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