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2.A.9.3.1
60 kDa inner membrane protein, YidC (involved in insertion of a wide range of membrane proteins, including anaerobic respiratory complexes (Price and Driessen, 2008). The thrid TMS in YidC contacts the substrate protein (Yu et al., 2008).  YidC occupies the lateral gate of the SecYEG translocase and is sequentially displaced by the nascent membrane protein (Sachelaru et al. 2013).  Residues involved in interaction with the Sec translocon have been identified (Li et al. 2014). YidC acts as a flexible chaperone, facilitating LacY folding (Zhu et al. 2013; Hennon and Dalbey 2014).  The structure of the dimeric insertion pore associated with the translating ribosome has been solved (Kohler et al. 2009).  A single copy of YidC interacts with the ribosome at the ribosomal tunnel; a site for membrane protein insertion at the YidC protein-lipid interface has been identified (Wickles et al. 2014).  The crystal structure of full-length E. coli YidC revealed that a hydrophilic groove, formed by five transmembrane helices, is a conserved structural feature as compared to the previous YidC structure from Bacillus halodurans, which lacks a periplasmic domain. Structural mapping of the substrate- or Sec protein-contact sites suggested the importance of the groove for the YidC functions as a chaperone and an insertase (Hennon and Dalbey 2014).  The structure of the dimeric insertion pore associated with the translating ribosome has been solved (Kohler et al. 2009).  A single copy of YidC interacts with the ribosome at the ribosomal tunnel; a site for membrane protein insertion at the YidC protein-lipid interface has been identified (Wickles et al. 2014).  The crystal structure of full-length E. coli YidC revealed that a hydrophilic groove, formed by five transmembrane helices, is a conserved structural feature as compared to the previous YidC structure from Bacillus halodurans, which lacks a periplasmic domain. Structural mapping of the substrate- or Sec protein-contact sites suggested the importance of the groove for the YidC functions as a chaperone and an insertase (Kumazaki et al. 2014).

Accession Number:P25714
Protein Name:60IM aka YidC aka B3705
Length:548
Molecular Weight:61526.00
Species:Escherichia coli [83333]
Number of TMSs:3
Location1 / Topology2 / Orientation3: Cell inner membrane1 / Multi-pass membrane protein2
Substrate proteins

Cross database links:

Genevestigator: P25714
EchoBASE: EB1183
EcoGene: EG11197
eggNOG: COG0706
HEGENOM: HBG507812
DIP: DIP-12442N
RefSeq: AP_004087.1    NP_418161.1   
Entrez Gene ID: 948214   
Pfam: PF02096   
BioCyc: EcoCyc:YIDC    ECOL168927:B3705-MONOMER   
KEGG: ecj:JW3683    eco:b3705   

Gene Ontology

GO:0016021 C:integral to membrane
GO:0005886 C:plasma membrane
GO:0032977 F:membrane insertase activity
GO:0005515 F:protein binding
GO:0051205 P:protein insertion into membrane

References (13)

[1] “DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication.”  Burland V.D.et.al.   7686882
[2] “The complete genome sequence of Escherichia coli K-12.”  Blattner F.R.et.al.   9278503
[3] “Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110.”  Hayashi K.et.al.   16738553
[4] “Physical mapping and nucleotide sequence of the rnpA gene that encodes the protein component of ribonuclease P in Escherichia coli.”  Hansen F.G.et.al.   2415431
[5] “Membrane topology of the 60-kDa Oxa1p homologue from Escherichia coli.”  Saeaef A.et.al.   9804807
[6] “YidC, the Escherichia coli homologue of mitochondrial Oxa1p, is a component of the Sec translocase.”  Scotti P.A.et.al.   10675323
[7] “YidC mediates membrane protein insertion in bacteria.”  Samuelson J.C.et.al.   10949305
[8] “SecDFyajC forms a heterotetrameric complex with YidC.”  Nouwen N.et.al.   12068816
[9] “Targeting, insertion, and localization of Escherichia coli YidC.”  Urbanus M.L.et.al.   11821429
[10] “A conserved function of YidC in the biogenesis of respiratory chain complexes.”  Van Der Laan M.et.al.   12724529
[11] “Defining the regions of Escherichia coli YidC that contribute to activity.”  Jiang F.et.al.   14506280
[12] “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.”  Yi L.et.al.   12950181
[13] “Protein complexes of the Escherichia coli cell envelope.”  Stenberg F.et.al.   16079137
Structure:
3BLC   3BS6   4UTQ   3wvf     

External Searches:

  • Search: DB with
  • BLAST ExPASy (Swiss Institute of Bioinformatics (SIB) BLAST)
  • CDD Search (Conserved Domain Database)
  • Search COGs (Clusters of Orthologous Groups of proteins)
  • 2° Structure (Network Protein Sequence Analysis)

Analyze:

Predict TMSs (Predict number of transmembrane segments)
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FASTA formatted sequence
1:	MDSQRNLLVI ALLFVSFMIW QAWEQDKNPQ PQAQQTTQTT TTAAGSAADQ GVPASGQGKL 
61:	ISVKTDVLDL TINTRGGDVE QALLPAYPKE LNSTQPFQLL ETSPQFIYQA QSGLTGRDGP 
121:	DNPANGPRPL YNVEKDAYVL AEGQNELQVP MTYTDAAGNT FTKTFVLKRG DYAVNVNYNV 
181:	QNAGEKPLEI SSFGQLKQSI TLPPHLDTGS SNFALHTFRG AAYSTPDEKY EKYKFDTIAD 
241:	NENLNISSKG GWVAMLQQYF ATAWIPHNDG TNNFYTANLG NGIAAIGYKS QPVLVQPGQT 
301:	GAMNSTLWVG PEIQDKMAAV APHLDLTVDY GWLWFISQPL FKLLKWIHSF VGNWGFSIII 
361:	ITFIVRGIMY PLTKAQYTSM AKMRMLQPKI QAMRERLGDD KQRISQEMMA LYKAEKVNPL 
421:	GGCFPLLIQM PIFLALYYML MGSVELRQAP FALWIHDLSA QDPYYILPIL MGVTMFFIQK 
481:	MSPTTVTDPM QQKIMTFMPV IFTVFFLWFP SGLVLYYIVS NLVTIIQQQL IYRGLEKRGL 
541:	HSREKKKS