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| | ==1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC== | | ==1.8 Angstrom crystal structure of the periplasmic domain of the membrane insertase YidC== |
| - | <StructureSection load='3bs6' size='340' side='right' caption='[[3bs6]], [[Resolution|resolution]] 1.80Å' scene=''> | + | <StructureSection load='3bs6' size='340' side='right'caption='[[3bs6]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3bs6]] is a 2 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BS6 FirstGlance]. <br> | + | <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><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene><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]] 1.8Å</td></tr> |
| - | <tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">oxaA, yidC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bs6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bs6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bs6 RCSB], [http://www.ebi.ac.uk/pdbsum/3bs6 PDBsum]</span></td></tr>
| + | </table> |
| - | <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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bs/3bs6_consurf.spt"</scriptWhenChecked> | + | <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/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </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/chain_selection.php?pdb_ID=2ata ConSurf]. | + | </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="clear:both"></div> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 3bs6" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Insertase|Insertase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Escherichia coli]] | | [[Category: Escherichia coli]] |
| - | [[Category: Ravaud, S.]] | + | [[Category: Large Structures]] |
| - | [[Category: Sinning, I.]] | + | [[Category: Ravaud S]] |
| - | [[Category: Beta supersandwich fold]] | + | [[Category: Sinning I]] |
| - | [[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]]
| + | |
| Structural highlights
3bs6 is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.8Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
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.[1] [2] [3] [4] [5] [6] [7] [8]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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.
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[9]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Scotti PA, Urbanus ML, Brunner J, de Gier JW, von Heijne G, van der Does C, Driessen AJ, Oudega B, Luirink J. YidC, the Escherichia coli homologue of mitochondrial Oxa1p, is a component of the Sec translocase. EMBO J. 2000 Feb 15;19(4):542-9. PMID:10675323 doi:http://dx.doi.org/10.1093/emboj/19.4.542
- ↑ Samuelson JC, Chen M, Jiang F, Moller I, Wiedmann M, Kuhn A, Phillips GJ, Dalbey RE. YidC mediates membrane protein insertion in bacteria. Nature. 2000 Aug 10;406(6796):637-41. PMID:10949305 doi:http://dx.doi.org/10.1038/35020586
- ↑ van der Laan M, Urbanus ML, Ten Hagen-Jongman CM, Nouwen N, Oudega B, Harms N, Driessen AJ, Luirink J. A conserved function of YidC in the biogenesis of respiratory chain complexes. Proc Natl Acad Sci U S A. 2003 May 13;100(10):5801-6. Epub 2003 Apr 30. PMID:12724529 doi:http://dx.doi.org/10.1073/pnas.0636761100
- ↑ Yi L, Jiang F, Chen M, Cain B, Bolhuis A, Dalbey RE. YidC is strictly required for membrane insertion of subunits a and c of the F(1)F(0)ATP synthase and SecE of the SecYEG translocase. Biochemistry. 2003 Sep 9;42(35):10537-44. PMID:12950181 doi:http://dx.doi.org/10.1021/bi034309h
- ↑ Froderberg L, Houben EN, Baars L, Luirink J, de Gier JW. Targeting and translocation of two lipoproteins in Escherichia coli via the SRP/Sec/YidC pathway. J Biol Chem. 2004 Jul 23;279(30):31026-32. Epub 2004 May 12. PMID:15140892 doi:10.1074/jbc.M403229200
- ↑ Nagamori S, Smirnova IN, Kaback HR. Role of YidC in folding of polytopic membrane proteins. J Cell Biol. 2004 Apr;165(1):53-62. Epub 2004 Apr 5. PMID:15067017 doi:http://dx.doi.org/10.1083/jcb.200402067
- ↑ Xie K, Kiefer D, Nagler G, Dalbey RE, Kuhn A. Different regions of the nonconserved large periplasmic domain of Escherichia coli YidC are involved in the SecF interaction and membrane insertase activity. Biochemistry. 2006 Nov 7;45(44):13401-8. PMID:17073462 doi:http://dx.doi.org/10.1021/bi060826z
- ↑ Wagner S, Pop OI, Haan GJ, Baars L, Koningstein G, Klepsch MM, Genevaux P, Luirink J, de Gier JW. Biogenesis of MalF and the MalFGK(2) maltose transport complex in Escherichia coli requires YidC. J Biol Chem. 2008 Jun 27;283(26):17881-90. doi: 10.1074/jbc.M801481200. Epub 2008, May 2. PMID:18456666 doi:http://dx.doi.org/10.1074/jbc.M801481200
- ↑ Ravaud S, Stjepanovic G, Wild K, Sinning I. The crystal structure of the periplasmic domain of the Escherichia coli membrane protein insertase YidC contains a substrate binding cleft. J Biol Chem. 2008 Apr 4;283(14):9350-8. Epub 2008 Jan 30. PMID:18234665 doi:10.1074/jbc.M710493200
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