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Protein

Outer membrane protein assembly factor BamD

Gene

bamD

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

Functioni

Part of the outer membrane protein assembly complex (Bam), which is involved in assembly and insertion of beta-barrel proteins into the outer membrane. Constitutes, with BamA, the core component of the assembly machinery. Probably involved in transient protein interactions. Efficient substrate folding and insertion into the outer membrane requires all 5 subunits (PubMed:20378773, PubMed:21823654, PubMed:27686148). A lateral gate may open between the first and last strands of the BamA beta-barrel that allows substrate to insert into the outer membrane; comparison of the structures of complete and nearly complete Bam complexes show there is considerable movement of all 5 proteins (PubMed:27686148, PubMed:26900875, PubMed:26901871, PubMed:26744406).9 Publications

GO - Biological processi

  • Gram-negative-bacterium-type cell outer membrane assembly Source: EcoCyc
  • protein insertion into membrane Source: EcoCyc

Enzyme and pathway databases

BioCyciEcoCyc:G7352-MONOMER.

Protein family/group databases

TCDBi1.B.33.1.3. the outer membrane protein insertion porin (bam complex) (ompip) family.

Names & Taxonomyi

Protein namesi
Recommended name:
Outer membrane protein assembly factor BamDUniRule annotation
Gene namesi
Name:bamDUniRule annotation
Synonyms:yfiO
Ordered Locus Names:b2595, JW2577
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG14222. bamD.

Subcellular locationi

GO - Cellular componenti

  • Bam protein complex Source: EcoCyc

Keywords - Cellular componenti

Cell outer membrane, Membrane

Pathology & Biotechi

Disruption phenotypei

Depletion decreases the density of outer membrane proteins, but does not significantly affect transport of lipopolysaccharides to the outer membrane.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 19UniRule annotationAdd BLAST19
ChainiPRO_000003622620 – 245Outer membrane protein assembly factor BamDAdd BLAST226

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi20N-palmitoyl cysteine1 Publication1
Lipidationi20S-diacylglycerol cysteine1 Publication1

Keywords - PTMi

Lipoprotein, Palmitate

Proteomic databases

PaxDbiP0AC02.
PRIDEiP0AC02.

Interactioni

Subunit structurei

Part of the Bam complex, which is composed of the outer membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE. Forms a subcomplex with BamC and BamE. Interacts directly with BamA. The Bam complex has the shape of a hat, with the BamA beta-barrel crown in the outer membrane and the periplasmic brim formed by the BamA POTRA domains and the 4 lipoproteins (PubMed:27686148, PubMed:26900875, PubMed:26901871, PubMed:26744406).12 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi4260615. 263 interactors.
851422. 1 interactor.
DIPiDIP-51120N.
IntActiP0AC02. 6 interactors.
MINTiMINT-8141303.
STRINGi316385.ECDH10B_2763.

Structurei

Secondary structure

1245
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi32 – 45Combined sources14
Helixi48 – 61Combined sources14
Helixi68 – 81Combined sources14
Helixi85 – 98Combined sources14
Beta strandi100 – 102Combined sources3
Helixi105 – 120Combined sources16
Turni126 – 129Combined sources4
Beta strandi133 – 135Combined sources3
Helixi138 – 151Combined sources14
Helixi160 – 188Combined sources29
Helixi191 – 204Combined sources14
Helixi209 – 224Combined sources16
Helixi228 – 240Combined sources13

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2YHCX-ray1.80A29-245[»]
3Q5MX-ray2.60A23-245[»]
3TGOX-ray2.90A/B21-245[»]
5AYWX-ray3.56D20-245[»]
5D0OX-ray2.90D1-245[»]
5D0QX-ray3.50D/H1-245[»]
5EKQX-ray3.39D20-245[»]
5LJOelectron microscopy4.90D26-243[»]
ProteinModelPortaliP0AC02.
SMRiP0AC02.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domaini

The N-terminal may interact with various proteins as a chaperone to assist in the folding and insertion of proteins into the outer membrane. The C-terminal region may serve as the link between BamA, BamC and BamE.1 Publication

Sequence similaritiesi

Belongs to the BamD family.UniRule annotation

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiENOG4106SNF. Bacteria.
COG4105. LUCA.
HOGENOMiHOG000260923.
InParanoidiP0AC02.
KOiK05807.
PhylomeDBiP0AC02.

Family and domain databases

CDDicd15830. BamD. 1 hit.
HAMAPiMF_00922. OM_assembly_BamD. 1 hit.
InterProiView protein in InterPro
IPR017689. BamD.
IPR011990. TPR-like_helical_dom.
SUPFAMiSSF48452. SSF48452. 1 hit.
TIGRFAMsiTIGR03302. OM_YfiO. 1 hit.
PROSITEiView protein in PROSITE
PS51257. PROKAR_LIPOPROTEIN. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0AC02-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTRMKYLVAA ATLSLFLAGC SGSKEEVPDN PPNEIYATAQ QKLQDGNWRQ
60 70 80 90 100
AITQLEALDN RYPFGPYSQQ VQLDLIYAYY KNADLPLAQA AIDRFIRLNP
110 120 130 140 150
THPNIDYVMY MRGLTNMALD DSALQGFFGV DRSDRDPQHA RAAFSDFSKL
160 170 180 190 200
VRGYPNSQYT TDATKRLVFL KDRLAKYEYS VAEYYTERGA WVAVVNRVEG
210 220 230 240
MLRDYPDTQA TRDALPLMEN AYRQMQMNAQ AEKVAKIIAA NSSNT
Length:245
Mass (Da):27,829
Last modified:November 8, 2005 - v1
Checksum:i91D0A25E69248C49
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti59D → Y in CAA94434 (Ref. 4) Curated1

Mass spectrometryi

Molecular mass is 26582 Da from positions 20 - 245. Determined by ESI. With 3 palmitic acid (C16) acyl chains.1 Publication
Molecular mass is 26603 Da from positions 20 - 245. Determined by ESI. With 2 palmitic (C16) and 1 stearic (C18) acid acyl chains.1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75644.1.
AP009048 Genomic DNA. Translation: BAA16480.1.
Z70523 Genomic DNA. Translation: CAA94434.1.
PIRiF65037.
RefSeqiNP_417086.1. NC_000913.3.
WP_000197686.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75644; AAC75644; b2595.
BAA16480; BAA16480; BAA16480.
GeneIDi947086.
KEGGiecj:JW2577.
eco:b2595.
PATRICifig|1411691.4.peg.4142.

Similar proteinsi

Entry informationi

Entry nameiBAMD_ECOLI
AccessioniPrimary (citable) accession number: P0AC02
Secondary accession number(s): P77146, Q47344
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 8, 2005
Last sequence update: November 8, 2005
Last modified: September 27, 2017
This is version 97 of the entry and version 1 of the sequence. See 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
  4. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries