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Protein

Membrane protein insertase YidC

Gene

yidC

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.8 Publications

GO - Molecular functioni

  • membrane insertase activity Source: EcoCyc

GO - Biological processi

  • protein complex assembly Source: UniProtKB
  • protein folding Source: UniProtKB
  • protein homooligomerization Source: EcoCyc
  • protein insertion into membrane Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Chaperone

Keywords - Biological processi

Protein transport, Transport

Enzyme and pathway databases

BioCyciEcoCyc:YIDC.
ECOL316407:JW3683-MONOMER.

Protein family/group databases

TCDBi2.A.9.3.1. the membrane protein insertase (yidc/alb3/oxa1) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Membrane protein insertase YidC
Alternative name(s):
Foldase YidC
Inner membrane protein YidC
Membrane integrase YidC
Oxa1Ec
Gene namesi
Name:yidC
Ordered Locus Names:b3705, JW3683
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11197. yidC.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 5CytoplasmicCurated5
Transmembranei6 – 23HelicalCuratedAdd BLAST18
Topological domaini24 – 342PeriplasmicAdd BLAST319
Transmembranei343 – 370HelicalCuratedAdd BLAST28
Topological domaini371 – 416CytoplasmicAdd BLAST46
Transmembranei417 – 446HelicalCuratedAdd BLAST30
Topological domaini447 – 463PeriplasmicAdd BLAST17
Transmembranei464 – 481HelicalCuratedAdd BLAST18
Topological domaini482 – 493CytoplasmicAdd BLAST12
Transmembranei494 – 509HelicalCuratedAdd BLAST16
Topological domaini510 – 512Periplasmic3
Transmembranei513 – 535HelicalCuratedAdd BLAST23
Topological domaini536 – 548CytoplasmicAdd BLAST13

GO - Cellular componenti

  • integral component of membrane Source: UniProtKB
  • integral component of plasma membrane Source: EcoCyc
  • plasma membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

Pathology & Biotechi

Disruption phenotypei

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.4 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi24 – 27EQDK → IEGR: Cold-sensitive at 30 degrees Celsius; when associated with 334-W--G-338. Protein accumulates stably. 4
Mutagenesisi334 – 338WFISQ → LEVLFQG: Cold-sensitive at 30 degrees Celsius; when associated with 24-I--R-27. Protein accumulates stably. 1 Publication5
Mutagenesisi361I → S: Loss of function. 1 Publication1
Mutagenesisi436L → S: Loss of function. 1 Publication1
Mutagenesisi483 – 487PTTVT → LVPRGS: Temperature-sensitive at 42 degrees Celsius; when associated with 512-ENLYFQG. Protein is not stable. 1 Publication5
Mutagenesisi512G → ENLYFQG: Temperature-sensitive at 42 degrees Celsius; when associated with 483-L--S-487. Protein is not stable. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001247121 – 548Membrane protein insertase YidCAdd BLAST548

Proteomic databases

EPDiP25714.
PaxDbiP25714.
PRIDEiP25714.

Expressioni

Inductioni

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

Interactioni

Subunit structurei

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 (PubMed:16079137). Can be cross-linked to FtsH, in the larger FtsH/HflKC complex.5 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
VIIIP036235EBI-6400779,EBI-8482910From a different organism.

Protein-protein interaction databases

BioGridi4261511. 225 interactors.
DIPiDIP-12442N.
IntActiP25714. 31 interactors.
MINTiMINT-6477960.
STRINGi511145.b3705.

Structurei

Secondary structure

1548
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi60 – 64Combined sources5
Beta strandi69 – 73Combined sources5
Beta strandi78 – 90Combined sources13
Beta strandi95 – 103Combined sources9
Beta strandi106 – 116Combined sources11
Helixi123 – 125Combined sources3
Beta strandi136 – 139Combined sources4
Beta strandi145 – 154Combined sources10
Beta strandi160 – 168Combined sources9
Beta strandi173 – 181Combined sources9
Beta strandi184 – 186Combined sources3
Beta strandi188 – 201Combined sources14
Beta strandi220 – 224Combined sources5
Turni226 – 228Combined sources3
Beta strandi231 – 233Combined sources3
Helixi235 – 239Combined sources5
Beta strandi245 – 250Combined sources6
Beta strandi252 – 257Combined sources6
Beta strandi260 – 280Combined sources21
Beta strandi283 – 289Combined sources7
Beta strandi293 – 295Combined sources3
Beta strandi300 – 311Combined sources12
Helixi314 – 320Combined sources7
Helixi324 – 327Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3BLCX-ray2.50A/B26-340[»]
3BS6X-ray1.80A/B56-329[»]
4UTQelectron microscopy8.00A1-548[»]
ProteinModelPortaliP25714.
SMRiP25714.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP25714.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni24 – 264Can be removed without causing lethality, dispensible for M13 procoat processingAdd BLAST241
Regioni215 – 265Interaction with SecF; not required for insertion of a number of Sec-dependent or Sec-independent substratesAdd BLAST51
Regioni265 – 346Required for Sec-dependent and Sec-independent protein insertionAdd BLAST82
Regioni527 – 548Can be removed without causing lethality, dispensible for M13 procoat processingAdd BLAST22

Domaini

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.

Sequence similaritiesi

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

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4105DHW. Bacteria.
COG0706. LUCA.
HOGENOMiHOG000101822.
InParanoidiP25714.
KOiK03217.
OMAiKNDATHS.
PhylomeDBiP25714.

Family and domain databases

HAMAPiMF_01810. YidC_type1. 1 hit.
InterProiIPR019998. Membr_insert_YidC.
IPR028055. Membr_insert_YidC/Oxa1_C.
IPR028053. Membr_insert_YidC_N.
IPR001708. Membrane_insert_OXA1/ALB3/YidC.
[Graphical view]
PANTHERiPTHR12428. PTHR12428. 1 hit.
PfamiPF02096. 60KD_IMP. 1 hit.
PF14849. YidC_periplas. 1 hit.
[Graphical view]
PRINTSiPR00701. 60KDINNERMP.
PR01900. YIDCPROTEIN.
TIGRFAMsiTIGR03593. yidC_nterm. 1 hit.
TIGR03592. yidC_oxa1_cterm. 1 hit.

Sequencei

Sequence statusi: Complete.

P25714-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDSQRNLLVI ALLFVSFMIW QAWEQDKNPQ PQAQQTTQTT TTAAGSAADQ
60 70 80 90 100
GVPASGQGKL ISVKTDVLDL TINTRGGDVE QALLPAYPKE LNSTQPFQLL
110 120 130 140 150
ETSPQFIYQA QSGLTGRDGP DNPANGPRPL YNVEKDAYVL AEGQNELQVP
160 170 180 190 200
MTYTDAAGNT FTKTFVLKRG DYAVNVNYNV QNAGEKPLEI SSFGQLKQSI
210 220 230 240 250
TLPPHLDTGS SNFALHTFRG AAYSTPDEKY EKYKFDTIAD NENLNISSKG
260 270 280 290 300
GWVAMLQQYF ATAWIPHNDG TNNFYTANLG NGIAAIGYKS QPVLVQPGQT
310 320 330 340 350
GAMNSTLWVG PEIQDKMAAV APHLDLTVDY GWLWFISQPL FKLLKWIHSF
360 370 380 390 400
VGNWGFSIII ITFIVRGIMY PLTKAQYTSM AKMRMLQPKI QAMRERLGDD
410 420 430 440 450
KQRISQEMMA LYKAEKVNPL GGCFPLLIQM PIFLALYYML MGSVELRQAP
460 470 480 490 500
FALWIHDLSA QDPYYILPIL MGVTMFFIQK MSPTTVTDPM QQKIMTFMPV
510 520 530 540
IFTVFFLWFP SGLVLYYIVS NLVTIIQQQL IYRGLEKRGL HSREKKKS
Length:548
Mass (Da):61,526
Last modified:July 1, 1993 - v2
Checksum:i95EBC5DAB4F2FCFB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L10328 Genomic DNA. Translation: AAA62056.1.
U00096 Genomic DNA. Translation: AAC76728.1.
AP009048 Genomic DNA. Translation: BAE77588.1.
M11056 Genomic DNA. No translation available.
PIRiB65173.
RefSeqiNP_418161.1. NC_000913.3.
WP_000378250.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76728; AAC76728; b3705.
BAE77588; BAE77588; BAE77588.
GeneIDi948214.
KEGGiecj:JW3683.
eco:b3705.
PATRICi32122907. VBIEscCol129921_3829.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L10328 Genomic DNA. Translation: AAA62056.1.
U00096 Genomic DNA. Translation: AAC76728.1.
AP009048 Genomic DNA. Translation: BAE77588.1.
M11056 Genomic DNA. No translation available.
PIRiB65173.
RefSeqiNP_418161.1. NC_000913.3.
WP_000378250.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3BLCX-ray2.50A/B26-340[»]
3BS6X-ray1.80A/B56-329[»]
4UTQelectron microscopy8.00A1-548[»]
ProteinModelPortaliP25714.
SMRiP25714.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261511. 225 interactors.
DIPiDIP-12442N.
IntActiP25714. 31 interactors.
MINTiMINT-6477960.
STRINGi511145.b3705.

Protein family/group databases

TCDBi2.A.9.3.1. the membrane protein insertase (yidc/alb3/oxa1) family.

Proteomic databases

EPDiP25714.
PaxDbiP25714.
PRIDEiP25714.

Protocols and materials databases

DNASUi948214.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76728; AAC76728; b3705.
BAE77588; BAE77588; BAE77588.
GeneIDi948214.
KEGGiecj:JW3683.
eco:b3705.
PATRICi32122907. VBIEscCol129921_3829.

Organism-specific databases

EchoBASEiEB1183.
EcoGeneiEG11197. yidC.

Phylogenomic databases

eggNOGiENOG4105DHW. Bacteria.
COG0706. LUCA.
HOGENOMiHOG000101822.
InParanoidiP25714.
KOiK03217.
OMAiKNDATHS.
PhylomeDBiP25714.

Enzyme and pathway databases

BioCyciEcoCyc:YIDC.
ECOL316407:JW3683-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP25714.
PROiP25714.

Family and domain databases

HAMAPiMF_01810. YidC_type1. 1 hit.
InterProiIPR019998. Membr_insert_YidC.
IPR028055. Membr_insert_YidC/Oxa1_C.
IPR028053. Membr_insert_YidC_N.
IPR001708. Membrane_insert_OXA1/ALB3/YidC.
[Graphical view]
PANTHERiPTHR12428. PTHR12428. 1 hit.
PfamiPF02096. 60KD_IMP. 1 hit.
PF14849. YidC_periplas. 1 hit.
[Graphical view]
PRINTSiPR00701. 60KDINNERMP.
PR01900. YIDCPROTEIN.
TIGRFAMsiTIGR03593. yidC_nterm. 1 hit.
TIGR03592. yidC_oxa1_cterm. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiYIDC_ECOLI
AccessioniPrimary (citable) accession number: P25714
Secondary accession number(s): Q2M818
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: July 1, 1993
Last modified: November 2, 2016
This is version 132 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.