6al2

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Crystal structure of E. coli YidC at 2.8 A resolution

Structural highlights

6al2 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 2.8Å
Ligands:OLC
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

YidC/Alb3/Oxa1 family proteins are involved in the insertion and assembly of membrane proteins. The core five transmembrane regions of YidC, which are conserved in the protein family, form a positively charged cavity open to the cytoplasmic side. The cavity plays an important role in membrane protein insertion. In all reported structural studies of YidC, the second cytoplasmic loop (C2 loop) was disordered, limiting the understanding of its role. Here, we determined the crystal structure of YidC including the C2 loop at 2.8A resolution with R/Rfree=21.8/27.5. This structure and subsequent molecular dynamics simulation indicated that the intrinsic flexible C2 loop covered the positively charged cavity. This crystal structure provides the coordinates of the complete core region including the C2 loop, which is valuable for further analyses of YidC.

2.8-A crystal structure of Escherichia coli YidC revealing all core regions, including flexible C2 loop.,Tanaka Y, Izumioka A, Abdul Hamid A, Fujii A, Haruyama T, Furukawa A, Tsukazaki T Biochem Biophys Res Commun. 2018 Oct 20;505(1):141-145. doi:, 10.1016/j.bbrc.2018.09.043. Epub 2018 Sep 18. PMID:30241934[9]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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Citations
3 reviews cite this structure
Structural and molecular mechanisms for membrane protein biogenesis by the Oxa1 superfamily.
McDowell et al. (2021)
2 more
3 other articles
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See Also

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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
  4. ↑ 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
  5. ↑ 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
  6. ↑ 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
  7. ↑ 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
  8. ↑ 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
  9. ↑ Tanaka Y, Izumioka A, Abdul Hamid A, Fujii A, Haruyama T, Furukawa A, Tsukazaki T. 2.8-A crystal structure of Escherichia coli YidC revealing all core regions, including flexible C2 loop. Biochem Biophys Res Commun. 2018 Oct 20;505(1):141-145. doi:, 10.1016/j.bbrc.2018.09.043. Epub 2018 Sep 18. PMID:30241934 doi:http://dx.doi.org/10.1016/j.bbrc.2018.09.043

Contents


PDB ID 6al2

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