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| | <StructureSection load='3blc' size='340' side='right'caption='[[3blc]], [[Resolution|resolution]] 2.50Å' scene=''> | | <StructureSection load='3blc' size='340' side='right'caption='[[3blc]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3blc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BLC FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3blc]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BLC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BLC FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">oxaA, yidC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=3blc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blc OCA], [https://pdbe.org/3blc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3blc RCSB], [https://www.ebi.ac.uk/pdbsum/3blc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3blc 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=3blc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3blc OCA], [https://pdbe.org/3blc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3blc RCSB], [https://www.ebi.ac.uk/pdbsum/3blc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3blc ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == 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>
| + | [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]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bl/3blc_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bl/3blc_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> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Oliver, D C]] | + | [[Category: Oliver DC]] |
| - | [[Category: Paetzel, M]] | + | [[Category: Paetzel M]] |
| - | [[Category: Chaperone]]
| + | |
| - | [[Category: Inner membrane]]
| + | |
| - | [[Category: Membrane assembly facilitator]]
| + | |
| - | [[Category: Oxaa]]
| + | |
| - | [[Category: Periplasmic domain]]
| + | |
| - | [[Category: Protein transport]]
| + | |
| - | [[Category: Transmembrane]]
| + | |
| - | [[Category: Yidc]]
| + | |
| Structural highlights
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
The essential bacterial membrane protein YidC facilitates insertion and assembly of proteins destined for integration into the inner membrane. It has homologues in both mitochondria and chloroplasts. Here we report the crystal structure of the Escherichia coli YidC major periplasmic domain (YidCECP1) at 2.5A resolution. This domain is present in YidC from Gram-negative bacteria and is more than half the size of the full-length protein. The structure reveals that YidCECP1 is made up of a large twisted beta-sandwich protein fold with a C-terminal alpha-helix that packs against one face of the beta-sandwich. Our structure and sequence analysis reveals that the C-terminal alpha-helix and the beta-sheet that it lays against are the most conserved regions of the domain. The region corresponding to the C-terminal alpha-helix was previously shown to be important for the protein insertase function of YidC and is conserved in other YidC-like proteins. The structure reveals that a region of YidC that was previously shown to be involved in binding to SecF maps to one edge of the beta-sandwich. Electrostatic analysis of the molecular surface for this region of YidC reveals a predominantly charged surface and suggests that the SecF-YidC interaction may be electrostatic in nature. Interestingly, YidCECP1 has significant structural similarity to galactose mutarotase from Lactococcus lactis, suggesting that this domain may have another function besides its role in membrane protein assembly.
Crystal structure of the major periplasmic domain of the bacterial membrane protein assembly facilitator YidC.,Oliver DC, Paetzel M J Biol Chem. 2008 Feb 22;283(8):5208-16. Epub 2007 Dec 19. PMID:18093969[9]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
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
- ↑ Oliver DC, Paetzel M. Crystal structure of the major periplasmic domain of the bacterial membrane protein assembly facilitator YidC. J Biol Chem. 2008 Feb 22;283(8):5208-16. Epub 2007 Dec 19. PMID:18093969 doi:10.1074/jbc.M708936200
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