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4utq

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A structural model of the active ribosome-bound membrane protein insertase YidC

4utq, resolution 8.00Å

Structural highlights

4utq 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:	Electron Microscopy, Resolution 8Å
Experimental data:	Check to display Experimental Data
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]

Publication Abstract from PubMed

The integration of most membrane proteins into the cytoplasmic membrane of bacteria occurs co-translationally. The universally conserved YidC protein mediates this process either individually as a membrane protein insertase, or in concert with the SecY complex. Here, we present a structural model of YidC based on evolutionary co-variation analysis, lipid-versus-protein-exposure and molecular dynamics simulations. The model suggests a distinctive arrangement of the conserved five transmembrane domains and a helical hairpin between transmembrane segment 2 (TM2) and TM3 on the cytoplasmic membrane surface. The model was used for docking into a cryo-electron microscopy reconstruction of a translating YidC-ribosome complex carrying the YidC substrate FOc. This structure reveals how a single copy of YidC interacts with the ribosome at the ribosomal tunnel exit and identifies a site for membrane protein insertion at the YidC protein-lipid interface. Together, these data suggest a mechanism for the co-translational mode of YidC-mediated membrane protein insertion.

A structural model of the active ribosome-bound membrane protein insertase YidC.,Wickles S, Singharoy A, Andreani J, Seemayer S, Bischoff L, Berninghausen O, Soeding J, Schulten K, van der Sluis EO, Beckmann R Elife (Cambridge). 2014 Jul 10:e03035. doi: 10.7554/eLife.03035. PMID:25012291^[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
↑ Wickles S, Singharoy A, Andreani J, Seemayer S, Bischoff L, Berninghausen O, Soeding J, Schulten K, van der Sluis EO, Beckmann R. A structural model of the active ribosome-bound membrane protein insertase YidC. Elife (Cambridge). 2014 Jul 10:e03035. doi: 10.7554/eLife.03035. PMID:25012291 doi:http://dx.doi.org/10.7554/eLife.03035

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4utq"

@@ Line 1: / Line 1: @@
 ==A structural model of the active ribosome-bound membrane protein insertase YidC==
-<StructureSection load='4utq' size='340' side='right' caption='[[4utq]], [[Resolution|resolution]] 8.00&Aring;' scene=''>
+<SX load='4utq' size='340' side='right' viewer='molstar' caption='[[4utq]], [[Resolution|resolution]] 8.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4utq]] 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=4UTQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UTQ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4utq]] 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=4UTQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UTQ FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4utq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4utq OCA], [http://pdbe.org/4utq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4utq RCSB], [http://www.ebi.ac.uk/pdbsum/4utq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4utq ProSAT]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 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=4utq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4utq OCA], [https://pdbe.org/4utq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4utq RCSB], [https://www.ebi.ac.uk/pdbsum/4utq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4utq ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>  [[http://www.uniprot.org/uniprot/ATPL_ECOLI ATPL_ECOLI]] F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation.[HAMAP-Rule:MF_01396]  Key component of the F(0) channel; it plays a direct role in translocation across the membrane. A homomeric c-ring of 10 subunits forms the central stalk rotor element with the F(1) delta and epsilon subunits.[HAMAP-Rule:MF_01396]
+[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>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 20: @@
 ==See Also==
-*[[ATPase|ATPase]]
+*[[ATPase 3D structures|ATPase 3D structures]]
+*[[Insertase|Insertase]]
 == References ==
 <references/>
 __TOC__
-</StructureSection>
+</SX>
 [[Category: Escherichia coli]]
-[[Category: Andreani, J]]
+[[Category: Large Structures]]
-[[Category: Beckmann, R]]
+[[Category: Andreani J]]
-[[Category: Berninghausen, O]]
+[[Category: Beckmann R]]
-[[Category: Bischoff, L]]
+[[Category: Berninghausen O]]
-[[Category: Schulten, K]]
+[[Category: Bischoff L]]
-[[Category: Seemayer, S]]
+[[Category: Schulten K]]
-[[Category: Singharoy, A]]
+[[Category: Seemayer S]]
-[[Category: Soeding, J]]
+[[Category: Singharoy A]]
-[[Category: Wickles, S]]
+[[Category: Soeding J]]
-[[Category: VanderSluis, E O]]
+[[Category: Wickles S]]
-[[Category: Bioinformatic]]
+[[Category: VanderSluis EO]]
-[[Category: Md simulation]]
-[[Category: Membrane]]
-[[Category: Protein translocation]]
-[[Category: Protein transport]]

4utq

From Proteopedia

Current revision

A structural model of the active ribosome-bound membrane protein insertase YidC

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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