2ral: Difference between revisions

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-{{Seed}}
-[[Image:2ral.png|left|200px]]
-<!--
+==Crystal Structure Analysis of double cysteine mutant of S.epidermidis adhesin SdrG: Evidence for the Dock,Lock and Latch ligand binding mechanism==
-The line below this paragraph, containing "STRUCTURE_2ral", creates the "Structure Box" on the page.
+<StructureSection load='2ral' size='340' side='right'caption='[[2ral]], [[Resolution|resolution]] 2.80&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'>[[2ral]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RAL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RAL 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]] 2.8&#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=2ral FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ral OCA], [https://pdbe.org/2ral PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ral RCSB], [https://www.ebi.ac.uk/pdbsum/2ral PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ral ProSAT]</span></td></tr>
-{{STRUCTURE_2ral|  PDB=2ral  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SDRG_STAEP SDRG_STAEP] Binds to the N-terminus of the B beta-chain of human fibrinogen and thereby interferes with thrombin cleavage and release of fibrinopeptide B, thus interfering with fibrin clot formation. This may hinder host defense against microbial infections.<ref>PMID:11371571</ref>
+== 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/ra/2ral_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2ral ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Staphylococcus epidermidis is an opportunistic pathogen and a major cause of foreign body infections. The S. epidermidis fibrinogen (Fg)-binding adhesin SdrG is necessary and sufficient for the attachment of this pathogen to Fg-coated materials. Based largely on structural analyses of the ligand binding domain of SdrG as an apo-protein and in complex with a Fg-like peptide, we proposed that SdrG follows a "dock, lock, and latch" mechanism to bind to Fg. This binding mechanism involves the docking of the ligand in a pocket formed between two SdrG subdomains followed by the movement of a C-terminal extension of one subdomain to cover the ligand and to insert and complement a beta-sheet in a neighboring subdomain. These proposed events result in a greatly stabilized closed conformation of the MSCRAMM-ligand complex. In this report, we describe a biochemical analysis of the proposed conformational changes that SdrG undergoes upon binding to its ligand. We have introduced disulfide bonds into SdrG to stabilize the open and closed forms of the apo-form of the MSCRAMM. We show that the stabilized closed form does not bind to the ligand and that binding can be restored in the presence of reducing agents such as dithiothreitol. We have also used Forster resonance energy transfer to dynamically show the conformational changes of SdrG upon binding to its ligand. Finally, we have used isothermic calorimetry to determine that hydrophobic interactions between the ligand and the protein are responsible for re-directing the C-terminal extension of the second subdomain required for triggering the beta-strand complementation event.
-===Crystal Structure Analysis of double cysteine mutant of S.epidermidis adhesin SdrG: Evidence for the Dock,Lock and Latch ligand binding mechanism===
+Evidence for the "dock, lock, and latch" ligand binding mechanism of the staphylococcal microbial surface component recognizing adhesive matrix molecules (MSCRAMM) SdrG.,Bowden MG, Heuck AP, Ponnuraj K, Kolosova E, Choe D, Gurusiddappa S, Narayana SV, Johnson AE, Hook M J Biol Chem. 2008 Jan 4;283(1):638-47. Epub 2007 Nov 8. PMID:17991749<ref>PMID:17991749</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_17991749}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2ral" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17991749 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17991749}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-RAL is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Staphylococcus_epidermidis Staphylococcus epidermidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RAL OCA].
-==Reference==
-Evidence for the "dock, lock, and latch" ligand binding mechanism of the staphylococcal microbial surface component recognizing adhesive matrix molecules (MSCRAMM) SdrG., Bowden MG, Heuck AP, Ponnuraj K, Kolosova E, Choe D, Gurusiddappa S, Narayana SV, Johnson AE, Hook M, J Biol Chem. 2008 Jan 4;283(1):638-47. Epub 2007 Nov 8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17991749 17991749]
 [[Category: Staphylococcus epidermidis]]
-[[Category: Pdbx_ordinal=, <PDBx:audit_author.]]
+[[Category: Bowden MG]]
-[[Category: Calcium]]
+[[Category: Hook M]]
-[[Category: Cell adhesion]]
+[[Category: Ponnuraj K]]
-[[Category: Cell wall]]
+[[Category: Sthanam N]]
-[[Category: Metal binding protein]]
-[[Category: Metal-binding]]
-[[Category: Mscramm]]
-[[Category: Peptidoglycan-anchor]]
-[[Category: Sdrg]]
-[[Category: Sdrg mutant]]
-[[Category: Secreted]]
-[[Category: Virulence]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec  3 20:06:42 2008''