Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

P25714 (YIDC_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 117. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Membrane protein insertase YidC
Alternative name(s):
Foldase YidC
Inner membrane protein YidC
Membrane integrase YidC
Oxa1Ec
Gene names
Name:yidC
Ordered Locus Names:b3705, JW3683
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length548 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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 F0ATP synthase, FtsQ and SecE proteins and for Sec-independent subunit c of the F0ATP 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 (MalFGK2) also requires YidC. Partially complements a Streptococcus mutans yidC2 disruption mutant. Ref.6 Ref.7 Ref.11 Ref.14 Ref.15 Ref.16 Ref.18 Ref.21

Subunit structure

Interacts with SecD and SecF. Component of the SecDFyajC complex, a heterotetrameric translocase complex. Specifically interacts with transmembrane segments of nascent integral membrane proteins during membrane integration. Found in 3 different complexes in inner membrane preparations (Ref.17). Can be cross-linked to FtsH, in the larger FtsH/HflKC complex. Ref.6 Ref.8 Ref.10 Ref.14 Ref.17 Ref.19

Subcellular location

Cell inner membrane; Multi-pass membrane protein. Note: Predominantly localized at cell poles at all stages of cell growth. Ref.9 Ref.17

Induction

At mid-exponential phase in strain MC4100 there are about 2500 copies per cell (at protein level). HAMAP-Rule MF_01810

Domain

Most of the large periplasmic domain (residues 24-264) is not required for either Sec-dependent or Sec-independent protein insertion. However, residues 265-346, the C-terminal part of the large periplasmic domain, are required for both Sec-dependent and Sec-independent protein insertion. Ref.18

Disruption phenotype

Lethality. Upon depletion experiments insertion of Sec translocase-independent integral membrane proteins ceases. Translocation of Sec-dependent protein decreases to a lesser extent. Also leads to decreased targeting and/or translocation of Lpp and BRP lipoproteins. Both spoIIIJ and yqjG of B.subtilis functionally complement yidC depletion, whereas Streptococcus mutans yidC1 and yidC2 only partially complement depletion. Ref.7 Ref.8 Ref.16 Ref.23

Sequence similarities

Belongs to the OXA1/ALB3/YidC family. Type 1 subfamily.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

VIIIP036235EBI-6400779,EBI-8482910From a different organism.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 548548Membrane protein insertase YidC HAMAP-Rule MF_01810
PRO_0000124712

Regions

Topological domain1 – 55Cytoplasmic Probable
Transmembrane6 – 2318Helical; Probable
Topological domain24 – 342319Periplasmic Ref.5 Ref.9
Transmembrane343 – 37028Helical; Probable
Topological domain371 – 41646Cytoplasmic Ref.5 Ref.9
Transmembrane417 – 44630Helical; Probable
Topological domain447 – 46317Periplasmic Ref.5 Ref.9
Transmembrane464 – 48118Helical; Probable
Topological domain482 – 49312Cytoplasmic Ref.5 Ref.9
Transmembrane494 – 50916Helical; Probable
Topological domain510 – 5123Periplasmic Ref.5 Ref.9
Transmembrane513 – 53523Helical; Probable
Topological domain536 – 54813Cytoplasmic Ref.5 Ref.9
Region24 – 264241Can be removed without causing lethality, dispensible for M13 procoat processing HAMAP-Rule MF_01810
Region215 – 26551Interacts with SecF; not required for insertion of a number of Sec-dependent or Sec-independent substrates HAMAP-Rule MF_01810
Region265 – 34682Required for Sec-dependent and Sec-independent protein insertion HAMAP-Rule MF_01810
Region527 – 54822Can be removed without causing lethality, dispensible for M13 procoat processing HAMAP-Rule MF_01810

Experimental info

Mutagenesis24 – 274EQDK → IEGR: Cold-sensitive at 30 degrees Celsius; when associated with 334-W--G-338. Protein accumulates stably.
Mutagenesis334 – 3385WFISQ → LEVLFQG: Cold-sensitive at 30 degrees Celsius; when associated with 24-I--R-27. Protein accumulates stably. Ref.12
Mutagenesis3611I → S: Loss of function. Ref.13
Mutagenesis4361L → S: Loss of function. Ref.13
Mutagenesis483 – 4875PTTVT → LVPRGS: Temperature-sensitive at 42 degrees Celsius; when associated with 512-ENLYFQG. Protein is not stable. Ref.12
Mutagenesis5121G → ENLYFQG: Temperature-sensitive at 42 degrees Celsius; when associated with 483-L--S-487. Protein is not stable. Ref.12

Secondary structure

................................................. 548
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P25714 [UniParc].

Last modified July 1, 1993. Version 2.
Checksum: 95EBC5DAB4F2FCFB

FASTA54861,526
        10         20         30         40         50         60 
MDSQRNLLVI ALLFVSFMIW QAWEQDKNPQ PQAQQTTQTT TTAAGSAADQ GVPASGQGKL 

        70         80         90        100        110        120 
ISVKTDVLDL TINTRGGDVE QALLPAYPKE LNSTQPFQLL ETSPQFIYQA QSGLTGRDGP 

       130        140        150        160        170        180 
DNPANGPRPL YNVEKDAYVL AEGQNELQVP MTYTDAAGNT FTKTFVLKRG DYAVNVNYNV 

       190        200        210        220        230        240 
QNAGEKPLEI SSFGQLKQSI TLPPHLDTGS SNFALHTFRG AAYSTPDEKY EKYKFDTIAD 

       250        260        270        280        290        300 
NENLNISSKG GWVAMLQQYF ATAWIPHNDG TNNFYTANLG NGIAAIGYKS QPVLVQPGQT 

       310        320        330        340        350        360 
GAMNSTLWVG PEIQDKMAAV APHLDLTVDY GWLWFISQPL FKLLKWIHSF VGNWGFSIII 

       370        380        390        400        410        420 
ITFIVRGIMY PLTKAQYTSM AKMRMLQPKI QAMRERLGDD KQRISQEMMA LYKAEKVNPL 

       430        440        450        460        470        480 
GGCFPLLIQM PIFLALYYML MGSVELRQAP FALWIHDLSA QDPYYILPIL MGVTMFFIQK 

       490        500        510        520        530        540 
MSPTTVTDPM QQKIMTFMPV IFTVFFLWFP SGLVLYYIVS NLVTIIQQQL IYRGLEKRGL 


HSREKKKS 

« Hide

References

« Hide 'large scale' references
[1]"DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication."
Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.
Genomics 16:551-561(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[2]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[3]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]"Physical mapping and nucleotide sequence of the rnpA gene that encodes the protein component of ribonuclease P in Escherichia coli."
Hansen F.G., Hansen E.B., Atlung T.
Gene 38:85-93(1985) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-3.
Strain: K12.
[5]"Membrane topology of the 60-kDa Oxa1p homologue from Escherichia coli."
Saaf A., Monne M., de Gier J.W., von Heijne G.
J. Biol. Chem. 273:30415-30418(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: TOPOLOGY.
Strain: K12/ MC1061 / TOP10F'.
[6]"YidC, the Escherichia coli homologue of mitochondrial Oxa1p, is a component of the Sec translocase."
Scotti P.A., Urbanus M.L., Brunner J., de Gier J.-W., von Heijne G., van der Does C., Driessen A.J.M., Oudega B., Luirink J.
EMBO J. 19:542-549(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN SEC-DEPENDENT PATHWAY, INTERACTION WITH TRANSMEMBRANE SEGMENTS.
[7]"YidC mediates membrane protein insertion in bacteria."
Samuelson J.C., Chen M., Jiang F., Moeller I., Wiedmann M., Kuhn A., Phillips G.J., Dalbey R.E.
Nature 406:637-641(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN SEC-INDEPENDENT PATHWAY, SUBSTRATES, DISRUPTION PHENOTYPE.
[8]"Sec-dependent membrane protein insertion: sequential interaction of nascent FtsQ with SecY and YidC."
Urbanus M.L., Scotti P.A., Froderberg L., Saaf A., de Gier J.W., Brunner J., Samuelson J.C., Dalbey R.E., Oudega B., Luirink J.
EMBO Rep. 2:524-529(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH FTSQ AFTER SECY, DISRUPTION PHENOTYPE.
[9]"Targeting, insertion, and localization of Escherichia coli YidC."
Urbanus M.L., Froederberg L., Drew D., Bjoerk P., de Gier J.-W., Brunner J., Oudega B., Luirink J.
J. Biol. Chem. 277:12718-12723(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: SRP- AND SEC-DEPENDENT INSERTION INTO MEMBRANES, SUBCELLULAR LOCATION, TOPOLOGY.
Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
[10]"SecDFyajC forms a heterotetrameric complex with YidC."
Nouwen N., Driessen A.J.M.
Mol. Microbiol. 44:1397-1405(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH SECD AND SECF.
[11]"A conserved function of YidC in the biogenesis of respiratory chain complexes."
Van Der Laan M., Urbanus M.L., Ten Hagen-Jongman C.M., Nouwen N., Oudega B., Harms N., Driessen A.J.M., Luirink J.
Proc. Natl. Acad. Sci. U.S.A. 100:5801-5806(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[12]"Conditional lethal mutations separate the M13 procoat and Pf3 coat functions of YidC: different YidC structural requirements for membrane protein insertion."
Chen M., Xie K., Nouwen N., Driessen A.J., Dalbey R.E.
J. Biol. Chem. 278:23295-23300(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF 23-TRP--LYS-27; 334-TRP--GLN-338; 483-PRO--THR-487 AND GLY-512.
[13]"Defining the regions of Escherichia coli YidC that contribute to activity."
Jiang F., Chen M., Yi L., de Gier J.-W.L., Kuhn A., Dalbey R.E.
J. Biol. Chem. 278:48965-48972(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF ILE-361 AND LEU-436.
[14]"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., Jiang F., Chen M., Cain B., Bolhuis A., Dalbey R.E.
Biochemistry 42:10537-10544(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, ATP SYNTHASE SUBUNIT AND SECE AS SUBSTRATES.
[15]"Targeting and translocation of two lipoproteins in Escherichia coli via the SRP/Sec/YidC pathway."
Froderberg L., Houben E.N., Baars L., Luirink J., de Gier J.W.
J. Biol. Chem. 279:31026-31032(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN TARGETING AND/OR TRANSLOCATION OF LIPOPROTEINS.
[16]"Role of YidC in folding of polytopic membrane proteins."
Nagamori S., Smirnova I.N., Kaback H.R.
J. Cell Biol. 165:53-62(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN FOLDING BUT NOT INSERTION OF LACY, DISRUPTION PHENOTYPE.
[17]"Protein complexes of the Escherichia coli cell envelope."
Stenberg F., Chovanec P., Maslen S.L., Robinson C.V., Ilag L., von Heijne G., Daley D.O.
J. Biol. Chem. 280:34409-34419(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT, SUBCELLULAR LOCATION.
Strain: BL21-DE3.
[18]"Different regions of the nonconserved large periplasmic domain of Escherichia coli YidC are involved in the SecF interaction and membrane insertase activity."
Xie K., Kiefer D., Nagler G., Dalbey R.E., Kuhn A.
Biochemistry 45:13401-13408(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION OF PERIPLASMIC DOMAIN.
[19]"Detection of cross-links between FtsH, YidC, HflK/C suggests a linked role for these proteins in quality control upon insertion of bacterial inner membrane proteins."
van Bloois E., Dekker H.L., Froderberg L., Houben E.N., Urbanus M.L., de Koster C.G., de Gier J.W., Luirink J.
FEBS Lett. 582:1419-1424(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH FTSH.
[20]"Functional overlap but lack of complete cross-complementation of Streptococcus mutans and Escherichia coli YidC orthologs."
Dong Y., Palmer S.R., Hasona A., Nagamori S., Kaback H.R., Dalbey R.E., Brady L.J.
J. Bacteriol. 190:2458-2469(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: COMPLEMENTATION BY AND IN STREPTOCOCCUS MUTANS.
[21]"Biogenesis of MalF and the MalFGK(2) maltose transport complex in Escherichia coli requires YidC."
Wagner S., Pop O.I., Haan G.J., Baars L., Koningstein G., Klepsch M.M., Genevaux P., Luirink J., de Gier J.W.
J. Biol. Chem. 283:17881-17890(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN FOLDING BUT NOT INSERTION OF MALF OR OF MALFGK(2) COMPLEX.
[22]"Bacillus subtilis SpoIIIJ and YqjG function in membrane protein biogenesis."
Saller M.J., Fusetti F., Driessen A.J.
J. Bacteriol. 191:6749-6757(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: COMPLEMENTATION BY SPOIIIJ AND YQJG OF B.SUBTILIS.
[23]"Membrane localization of small proteins in Escherichia coli."
Fontaine F., Fuchs R.T., Storz G.
J. Biol. Chem. 286:32464-32474(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: DISRUPTION PHENOTYPE.
Strain: K12 / MG1655 / ATCC 47076.
[24]"Crystal structure of the major periplasmic domain of the bacterial membrane protein assembly facilitator YidC."
Oliver D.C., Paetzel M.
J. Biol. Chem. 283:5208-5216(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 26-340.
Strain: K12.
[25]"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. 283:9350-9358(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 56-329.
[26]"Assembly of bacterial inner membrane proteins."
Dalbey R.E., Wang P., Kuhn A.
Annu. Rev. Biochem. 80:161-187(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L10328 Genomic DNA. Translation: AAA62056.1.
U00096 Genomic DNA. Translation: AAC76728.1.
AP009048 Genomic DNA. Translation: BAE77588.1.
M11056 Genomic DNA. No translation available.
PIRB65173.
RefSeqNP_418161.1. NC_000913.3.
YP_491729.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3BLCX-ray2.50A/B26-340[»]
3BS6X-ray1.80A/B56-329[»]
ProteinModelPortalP25714.
SMRP25714. Positions 59-329.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-12442N.
IntActP25714. 31 interactions.
MINTMINT-6477960.
STRING511145.b3705.

Protein family/group databases

TCDB2.A.9.3.1. the cytochrome oxidase biogenesis (oxa1) family.

Proteomic databases

PaxDbP25714.
PRIDEP25714.

Protocols and materials databases

DNASU948214.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76728; AAC76728; b3705.
BAE77588; BAE77588; BAE77588.
GeneID12932517.
948214.
KEGGecj:Y75_p3467.
eco:b3705.
PATRIC32122907. VBIEscCol129921_3829.

Organism-specific databases

EchoBASEEB1183.
EcoGeneEG11197. yidC.

Phylogenomic databases

eggNOGCOG0706.
HOGENOMHOG000101822.
KOK03217.
OMAGSSEPFQ.
OrthoDBEOG6X6RF2.
PhylomeDBP25714.
ProtClustDBPRK01318.

Enzyme and pathway databases

BioCycEcoCyc:YIDC.
ECOL316407:JW3683-MONOMER.

Gene expression databases

GenevestigatorP25714.

Family and domain databases

HAMAPMF_01810. YidC_type1.
InterProIPR019998. Membr_insert_YidC.
IPR028055. Membr_insert_YidC/Oxa1_C.
IPR028053. Membr_insert_YidC_N.
IPR001708. Membrane_insert_OXA1/ALB3/YidC.
[Graphical view]
PANTHERPTHR12428. PTHR12428. 1 hit.
PfamPF02096. 60KD_IMP. 1 hit.
PF14849. YidC_periplas. 1 hit.
[Graphical view]
PRINTSPR00701. 60KDINNERMP.
PR01900. YIDCPROTEIN.
TIGRFAMsTIGR03593. yidC_nterm. 1 hit.
TIGR03592. yidC_oxa1_cterm. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP25714.
PROP25714.

Entry information

Entry nameYIDC_ECOLI
AccessionPrimary (citable) accession number: P25714
Secondary accession number(s): Q2M818
Entry history
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: July 1, 1993
Last modified: April 16, 2014
This is version 117 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene