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| | ==Solution structure of a protein domain== | | ==Solution structure of a protein domain== |
| - | <StructureSection load='2mk5' size='340' side='right'caption='[[2mk5]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='2mk5' size='340' side='right'caption='[[2mk5]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2mk5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus_phage_gh15 Staphylococcus aureus phage gh15]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MK5 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2mk5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_phage_G15 Staphylococcus phage G15]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2MK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2MK5 FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[4olk|4olk]], [[4ols|4ols]]</div></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lysGH15, GH15_071 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=760530 Staphylococcus aureus phage GH15])</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=2mk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mk5 OCA], [https://pdbe.org/2mk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mk5 RCSB], [https://www.ebi.ac.uk/pdbsum/2mk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mk5 ProSAT]</span></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=2mk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2mk5 OCA], [https://pdbe.org/2mk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2mk5 RCSB], [https://www.ebi.ac.uk/pdbsum/2mk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2mk5 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/D6QY02_9CAUD D6QY02_9CAUD] |
| - | The lysin LysGH15, which is derived from the staphylococcal phage GH15, demonstrates a wide lytic spectrum and strong lytic activity against methicillin-resistant Staphylococcus aureus (MRSA). Here, we find that the lytic activity of the full-length LysGH15 and its CHAP domain is dependent on calcium ions. To elucidate the molecular mechanism, the structures of three individual domains of LysGH15 were determined. Unexpectedly, the crystal structure of the LysGH15 CHAP domain reveals an "EF-hand-like" calcium-binding site near the Cys-His-Glu-Asn quartet active site groove. To date, the calcium-binding site in the LysGH15 CHAP domain is unique among homologous proteins, and it represents the first reported calcium-binding site in the CHAP family. More importantly, the calcium ion plays an important role as a switch that modulates the CHAP domain between the active and inactive states. Structure-guided mutagenesis of the amidase-2 domain reveals that both the zinc ion and E282 are required in catalysis and enable us to propose a catalytic mechanism. Nuclear magnetic resonance (NMR) spectroscopy and titration-guided mutagenesis identify residues (e.g., N404, Y406, G407, and T408) in the SH3b domain that are involved in the interactions with the substrate. To the best of our knowledge, our results constitute the first structural information on the biochemical features of a staphylococcal phage lysin and represent a pivotal step forward in understanding this type of lysin.
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| - | Structural and biochemical characterization reveals LysGH15 as an unprecedented "EF-hand-like" calcium-binding phage lysin.,Gu J, Feng Y, Feng X, Sun C, Lei L, Ding W, Niu F, Jiao L, Yang M, Li Y, Liu X, Song J, Cui Z, Han D, Du C, Yang Y, Ouyang S, Liu ZJ, Han W PLoS Pathog. 2014 May 15;10(5):e1004109. doi: 10.1371/journal.ppat.1004109., eCollection 2014 May. PMID:24831957<ref>PMID:24831957</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 2mk5" style="background-color:#fffaf0;"></div>
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| | ==See Also== | | ==See Also== |
| - | *[[Lysin|Lysin]] | + | *[[Lysin 3D structures|Lysin 3D structures]] |
| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Staphylococcus aureus phage gh15]] | + | [[Category: Staphylococcus phage G15]] |
| - | [[Category: Feng, Y]] | + | [[Category: Feng Y]] |
| - | [[Category: Gu, J]] | + | [[Category: Gu J]] |
| - | [[Category: Hydrolase]]
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