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| | ==Crystal structure of human alpha_defensin-2 (variant GLY16->D-ALA), P 32 2 1 space group )== | | ==Crystal structure of human alpha_defensin-2 (variant GLY16->D-ALA), P 32 2 1 space group )== |
| - | <StructureSection load='1zmi' size='340' side='right' caption='[[1zmi]], [[Resolution|resolution]] 1.15Å' scene=''> | + | <StructureSection load='1zmi' size='340' side='right'caption='[[1zmi]], [[Resolution|resolution]] 1.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1zmi]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZMI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZMI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1zmi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZMI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZMI FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.15Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dfn|1dfn]], [[1zmh|1zmh]], [[1zmk|1zmk]], [[1zmm|1zmm]], [[1zmp|1zmp]], [[1zmq|1zmq]]</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=1zmi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zmi OCA], [https://pdbe.org/1zmi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zmi RCSB], [https://www.ebi.ac.uk/pdbsum/1zmi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zmi ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DEFA3, DEF3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
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| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1zmi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zmi OCA], [http://pdbe.org/1zmi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zmi RCSB], [http://www.ebi.ac.uk/pdbsum/1zmi PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DEF3_HUMAN DEF3_HUMAN]] Defensin 2 and defensin 3 have antibiotic, fungicide and antiviral activities. Has antimicrobial activity against Gram-negative and Gram-positive bacteria. Defensins are thought to kill microbes by permeabilizing their plasma membrane.<ref>PMID:15616305</ref> <ref>PMID:2006422</ref> <ref>PMID:15894545</ref> <ref>PMID:17452329</ref> | + | [https://www.uniprot.org/uniprot/DEF3_HUMAN DEF3_HUMAN] Defensin 2 and defensin 3 have antibiotic, fungicide and antiviral activities. Has antimicrobial activity against Gram-negative and Gram-positive bacteria. Defensins are thought to kill microbes by permeabilizing their plasma membrane.<ref>PMID:15616305</ref> <ref>PMID:2006422</ref> <ref>PMID:15894545</ref> <ref>PMID:17452329</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | ==See Also== | | ==See Also== |
| - | *[[Defensin|Defensin]] | + | *[[Defensin 3D structures|Defensin 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Human]] | + | [[Category: Homo sapiens]] |
| - | [[Category: Lu, W]] | + | [[Category: Large Structures]] |
| - | [[Category: Lubkowski, J]] | + | [[Category: Lu W]] |
| - | [[Category: Prahl, A]] | + | [[Category: Lubkowski J]] |
| - | [[Category: Alpha-defensin]] | + | [[Category: Prahl A]] |
| - | [[Category: Antimicrobial]]
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| - | [[Category: Antimicrobial protein]]
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| - | [[Category: D-amino acid substitution]]
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| Structural highlights
Function
DEF3_HUMAN Defensin 2 and defensin 3 have antibiotic, fungicide and antiviral activities. Has antimicrobial activity against Gram-negative and Gram-positive bacteria. Defensins are thought to kill microbes by permeabilizing their plasma membrane.[1] [2] [3] [4]
Publication Abstract from PubMed
Defensins are cationic antimicrobial mini-proteins that play important roles in the innate immune defense against microbial infection. Six invariant Cys residues in each defensin form three structurally indispensable intramolecular disulfide bridges. The only other residue invariant in all known mammalian defensins is a Gly. Structural studies indicate that the invariant Gly residue is located in an atypical, classic-type beta-bulge with the backbone torsion angles (Phi, Psi) disallowed for L-amino acids but permissible for D-enantiomers. We replaced the invariant Gly17 residue in human neutrophil alpha-defensin 2 (HNP2) by L-Ala or one of the D-amino acids Ala, Glu, Phe, Arg, Thr, Val, or Tyr. Although L-Ala17-HNP2 could not be folded, resulting in massive aggregation, all of the D-amino acid-substituted analogs folded with high efficiency. The high resolution x-ray crystal structures of dimeric D-Ala17-HNP2 were determined in three different crystal forms, showing a well preserved beta-bulge identical to those found in other defensins. The seven D-analogs of HNP2 exhibited highly variable bactericidal activity against Gram-positive and Gram-negative test strains, consistent with the premise that interplay between charge and hydrophobicity dictates how amphiphilic defensins kill. Further, the bactericidal activity of these d-amino acid analogs of HNP2 correlated well with their ability to induce leakage from large unilamellar vesicles, supporting membrane permeabilization as the lethal event in microbial killing by HNP2. Our findings identify a conformational prerequisite in the beta-bulge of defensins essential for correct folding and native structure, thereby explaining the molecular basis of the Gly-Xaa-Cys motif conserved in all mammalian defensins.
Reconstruction of the conserved beta-bulge in mammalian defensins using D-amino acids.,Xie C, Prahl A, Ericksen B, Wu Z, Zeng P, Li X, Lu WY, Lubkowski J, Lu W J Biol Chem. 2005 Sep 23;280(38):32921-9. Epub 2005 May 13. PMID:15894545[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Ericksen B, Wu Z, Lu W, Lehrer RI. Antibacterial activity and specificity of the six human {alpha}-defensins. Antimicrob Agents Chemother. 2005 Jan;49(1):269-75. PMID:15616305 doi:10.1128/AAC.49.1.269-275.2005
- ↑ Hill CP, Yee J, Selsted ME, Eisenberg D. Crystal structure of defensin HNP-3, an amphiphilic dimer: mechanisms of membrane permeabilization. Science. 1991 Mar 22;251(5000):1481-5. PMID:2006422
- ↑ Xie C, Prahl A, Ericksen B, Wu Z, Zeng P, Li X, Lu WY, Lubkowski J, Lu W. Reconstruction of the conserved beta-bulge in mammalian defensins using D-amino acids. J Biol Chem. 2005 Sep 23;280(38):32921-9. Epub 2005 May 13. PMID:15894545 doi:M503084200
- ↑ Zou G, de Leeuw E, Li C, Pazgier M, Li C, Zeng P, Lu WY, Lubkowski J, Lu W. Toward understanding the cationicity of defensins. Arg and Lys versus their noncoded analogs. J Biol Chem. 2007 Jul 6;282(27):19653-65. Epub 2007 Apr 23. PMID:17452329 doi:10.1074/jbc.M611003200
- ↑ Xie C, Prahl A, Ericksen B, Wu Z, Zeng P, Li X, Lu WY, Lubkowski J, Lu W. Reconstruction of the conserved beta-bulge in mammalian defensins using D-amino acids. J Biol Chem. 2005 Sep 23;280(38):32921-9. Epub 2005 May 13. PMID:15894545 doi:M503084200
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