3dgs: Difference between revisions

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-{{Seed}}
-[[Image:3dgs.jpg|left|200px]]
-<!--
+==Changing the determinants of protein stability from covalent to non-covalent interactions by in-vitro evolution: a structural and energetic analysis==
-The line below this paragraph, containing "STRUCTURE_3dgs", creates the "Structure Box" on the page.
+<StructureSection load='3dgs' size='340' side='right'caption='[[3dgs]], [[Resolution|resolution]] 1.90&Aring;' 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'>[[3dgs]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacteria_phage_fd Enterobacteria phage fd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DGS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DGS 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">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</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=3dgs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dgs OCA], [https://pdbe.org/3dgs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dgs RCSB], [https://www.ebi.ac.uk/pdbsum/3dgs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dgs ProSAT]</span></td></tr>
-{{STRUCTURE_3dgs|  PDB=3dgs  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/G3P_BPFD G3P_BPFD] Plays essential roles both in the penetration of the viral genome into the bacterial host via pilus retraction and in the extrusion process. During the initial step of infection, G3P mediates adsorption of the phage to its primary receptor, the tip of host F-pilus. Subsequent interaction with the host entry receptor tolA induces penetration of the viral DNA into the host cytoplasm. In the extrusion process, G3P mediates the release of the membrane-anchored virion from the cell via its C-terminal domain.<ref>PMID:12054858</ref> <ref>PMID:21110981</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The three disulfide bonds of the gene-3-protein of the phage fd are essential for the conformational stability of this protein, and it unfolds when they are removed by reduction or mutation. Previously, we used an iterative in vitro selection strategy to generate a stable and functional form of the gene-3-protein without these disulfides. It yielded optimal replacements for the disulfide bonds as well as several stabilizing second-site mutations. The best selected variant showed a higher thermal stability compared with the disulfide-bonded wild-type protein. Here, we investigated the molecular basis of this strong stabilization by solving the crystal structure of this variant and by analyzing the contributions to the conformational stability of the selected mutations individually. They could mostly be explained by improved side-chain packing. The R29W substitution alone increased the midpoint of the thermal unfolding transition by 14 deg and the conformational stability by about 25 kJ mol(-1). This key mutation (i) removed a charged side chain that forms a buried salt bridge in the disulfide-containing wild-type protein, (ii) optimized the local packing with the residues that replace the C46-C53 disulfide and (iii) improved the domain interactions. Apparently, certain residues in proteins indeed play key roles for stability.
-===Changing the determinants of protein stability from covalent to non-covalent interactions by in-vitro evolution: a structural and energetic analysis===
+Changing the determinants of protein stability from covalent to non-covalent interactions by in vitro evolution: a structural and energetic analysis.,Kather I, Jakob R, Dobbek H, Schmid FX J Mol Biol. 2008 Sep 12;381(4):1040-54. Epub 2008 Jul 2. PMID:18621056<ref>PMID:18621056</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3dgs" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-DGS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_fd Enterobacteria phage fd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DGS OCA].
+*[[G3p|G3p]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Enterobacteria phage fd]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Dobbek, H.]]
+[[Category: Dobbek H]]
-[[Category: Jakob, R P.]]
+[[Category: Jakob RP]]
-[[Category: Kather, I.]]
+[[Category: Kather I]]
-[[Category: Schmid, F X.]]
+[[Category: Schmid FX]]
-[[Category: Capsid protein]]
-[[Category: Dissulfide bond]]
-[[Category: Evolutionary protein design]]
-[[Category: Phage display]]
-[[Category: Phage gene-3-protein]]
-[[Category: Phage recognition]]
-[[Category: Protein stabilization]]
-[[Category: Viral protein]]
-[[Category: Virion]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 23 11:53:24 2008''