3bs6: Difference between revisions

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-[[Image:3bs6.jpg|left|200px]]<br /><applet load="3bs6" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="3bs6, resolution 1.800&Aring;" />
-'''1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC'''<br />
-==Overview==
+==1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC==
-In bacteria the biogenesis of inner membrane proteins requires targeting and insertion factors such as the signal recognition particle and the Sec-translocon. YidC is an essential membrane protein involved in the insertion of inner membrane proteins together with the Sec-translocon, but also as a separate entity. YidC of Escherichia coli is a member of the conserved YidC (in bacteria)/Oxa1 (in mitochondria)/Alb3 (in chloroplasts) protein family and contains six transmembrane segments and a large periplasmic domain (P1). We determined the crystal structure of the periplasmic domain of YidC from E.coli (P1D) at 1.8A resolution. The structure of P1D shows the conserved ss-supersandwich-fold of carbohydrate binding proteins and an a-helical linker region at the C-terminus that packs against the ss-supersandwich by a highly conserved interface. P1D exhibits an elongated cleft of similar architecture as found in the structural homologs. However the electrostatic properties and molecular details of the cleft make it unlikely to interact with carbohydrate substrates. The cleft in P1D is occupied by a polyethylene glycol molecule suggesting an elongated peptide or acyl chain as a natural ligand. The region of P1D previously reported to interact with SecF maps to a surface area in the vicinity of the cleft. The conserved C-terminal region of the P1 domain was reported to be essential for the membrane insertase function of YidC. The analysis of this region suggests a role in membrane interaction and/or in the regulation of YidC interaction with binding partners.
+<StructureSection load='3bs6' size='340' side='right'caption='[[3bs6]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3bs6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BS6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BS6 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></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=3bs6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bs6 OCA], [https://pdbe.org/3bs6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bs6 RCSB], [https://www.ebi.ac.uk/pdbsum/3bs6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bs6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/YIDC_ECOLI YIDC_ECOLI] Inner membrane protein required for the insertion and/or proper folding and/or complex formation of integral inner membrane proteins. Involved in integration of membrane proteins that insert dependently and independently of the Sec translocase complex, as well as at least 2 lipoproteins. Its own insertion requires SRP and is Sec translocase-dependent. Essential for the integration of Sec-dependent subunit a of the F(0)ATP synthase, FtsQ and SecE proteins and for Sec-independent subunit c of the F(0)ATP synthase, M13 phage procoat and the N-terminus of leader peptidase Lep. Probably interacts directly with Sec-independent substrates. Sec-dependent protein FtsQ interacts first with SecY then subsequently with YidC. Sec-dependent LacY and MalF require YidC to acquire tertiary structure and stability, a chaperone-like function, but not for membrane insertion. Stable maltose transport copmplex formation (MalFGK(2)) also requires YidC. Partially complements a Streptococcus mutans yidC2 disruption mutant.<ref>PMID:10675323</ref> <ref>PMID:10949305</ref> <ref>PMID:12724529</ref> <ref>PMID:12950181</ref> <ref>PMID:15140892</ref> <ref>PMID:15067017</ref> <ref>PMID:17073462</ref> <ref>PMID:18456666</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/bs/3bs6_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=3bs6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In bacteria the biogenesis of inner membrane proteins requires targeting and insertion factors such as the signal recognition particle and the Sec translocon. YidC is an essential membrane protein involved in the insertion of inner membrane proteins together with the Sec translocon, but also as a separate entity. YidC of Escherichia coli is a member of the conserved YidC (in bacteria)/Oxa1 (in mitochondria)/Alb3 (in chloroplasts) protein family and contains six transmembrane segments and a large periplasmic domain (P1). We determined the crystal structure of the periplasmic domain of YidC from E. coli (P1D) at 1.8 A resolution. The structure of P1D shows the conserved beta-supersandwich fold of carbohydrate-binding proteins and an alpha-helical linker region at the C terminus that packs against the beta-supersandwich by a highly conserved interface. P1D exhibits an elongated cleft of similar architecture as found in the structural homologs. However, the electrostatic properties and molecular details of the cleft make it unlikely to interact with carbohydrate substrates. The cleft in P1D is occupied by a polyethylene glycol molecule suggesting an elongated peptide or acyl chain as a natural ligand. The region of P1D previously reported to interact with SecF maps to a surface area in the vicinity of the cleft. The conserved C-terminal region of the P1 domain was reported to be essential for the membrane insertase function of YidC. The analysis of this region suggests a role in membrane interaction and/or in the regulation of YidC interaction with binding partners.
-==About this Structure==
+The crystal structure of the periplasmic domain of the Escherichia coli membrane protein insertase YidC contains a substrate binding cleft.,Ravaud S, Stjepanovic G, Wild K, Sinning I J Biol Chem. 2008 Apr 4;283(14):9350-8. Epub 2008 Jan 30. PMID:18234665<ref>PMID:18234665</ref>
-BS6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=CA:'>CA</scene>, <scene name='pdbligand=PG4:'>PG4</scene>, <scene name='pdbligand=PGE:'>PGE</scene>, <scene name='pdbligand=EDO:'>EDO</scene> and <scene name='pdbligand=2PE:'>2PE</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Sites: <scene name='pdbsite=AC1:Ca+Binding+Site+For+Residue+A+1'>AC1</scene>, <scene name='pdbsite=AC2:Ca+Binding+Site+For+Residue+A+2'>AC2</scene>, <scene name='pdbsite=AC3:Ca+Binding+Site+For+Residue+A+3'>AC3</scene>, <scene name='pdbsite=AC4:Ca+Binding+Site+For+Residue+A+4'>AC4</scene>, <scene name='pdbsite=AC5:Ca+Binding+Site+For+Residue+A+5'>AC5</scene>, <scene name='pdbsite=AC6:2pe+Binding+Site+For+Residue+B+1'>AC6</scene>, <scene name='pdbsite=AC7:Pg4+Binding+Site+For+Residue+A+336'>AC7</scene>, <scene name='pdbsite=AC8:Pge+Binding+Site+For+Residue+A+337'>AC8</scene>, <scene name='pdbsite=AC9:Pge+Binding+Site+For+Residue+B+336'>AC9</scene>, <scene name='pdbsite=BC1:Pge+Binding+Site+For+Residue+A+338'>BC1</scene>, <scene name='pdbsite=BC2:Edo+Binding+Site+For+Residue+B+337'>BC2</scene>, <scene name='pdbsite=BC3:Edo+Binding+Site+For+Residue+A+339'>BC3</scene>, <scene name='pdbsite=BC4:Edo+Binding+Site+For+Residue+B+3'>BC4</scene>, <scene name='pdbsite=BC5:Edo+Binding+Site+For+Residue+A+340'>BC5</scene>, <scene name='pdbsite=BC6:Edo+Binding+Site+For+Residue+B+6'>BC6</scene> and <scene name='pdbsite=BC7:Edo+Binding+Site+For+Residue+A+7'>BC7</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BS6 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-The crystal structure of the periplasmic domain of the Escherichia coli membrane protein insertase YidC contains a conserved substrate binding cleft., Ravaud S, Stjepanovic G, Wild K, Sinning I, J Biol Chem. 2008 Jan 30;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18234665 18234665]
+</div>
+<div class="pdbe-citations 3bs6" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Insertase|Insertase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Ravaud, S.]]
+[[Category: Ravaud S]]
-[[Category: Sinning, I.]]
+[[Category: Sinning I]]
-[[Category: 2PE]]
-[[Category: CA]]
-[[Category: EDO]]
-[[Category: PG4]]
-[[Category: PGE]]
-[[Category: beta supersandwich fold]]
-[[Category: chaperone]]
-[[Category: helical linker domain]]
-[[Category: membrane insertion]]
-[[Category: membrane protein]]
-[[Category: periplasmic domain]]
-[[Category: protein transport]]
-[[Category: sec translocon]]
-[[Category: yidc/oxa1/alb3 family]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:07:17 2008''