ID BAMD_ECOLI Reviewed; 245 AA.
AC P0AC02; P77146; Q47344;
DT 08-NOV-2005, integrated into UniProtKB/Swiss-Prot.
DT 08-NOV-2005, sequence version 1.
DT 10-MAY-2017, entry version 93.
DE RecName: Full=Outer membrane protein assembly factor BamD {ECO:0000255|HAMAP-Rule:MF_00922};
DE Flags: Precursor;
GN Name=bamD {ECO:0000255|HAMAP-Rule:MF_00922}; Synonyms=yfiO;
GN OrderedLocusNames=b2595, JW2577;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K.,
RA Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N.,
RA Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H.,
RA Oshima T., Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S.,
RA Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C.,
RA Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-
RT K12 genome corresponding to 50.0-68.8 min on the linkage map and
RT analysis of its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
RA Mau B., Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains
RT MG1655 and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 43-245.
RC STRAIN=K12;
RA Faber F., van Giezen M., van Gorcom R.F.M., Harder W.;
RT "Identification of two Escherichia coli K12 proteins which are induced
RT in response to pollutant stress.";
RL Submitted (APR-1996) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP SUBUNIT, AND IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=K12;
RX PubMed=15851030; DOI=10.1016/j.cell.2005.02.015;
RA Wu T., Malinverni J., Ruiz N., Kim S., Silhavy T.J., Kahne D.;
RT "Identification of a multicomponent complex required for outer
RT membrane biogenesis in Escherichia coli.";
RL Cell 121:235-245(2005).
RN [6]
RP SUBUNIT, AND SUBCELLULAR LOCATION.
RC STRAIN=BL21-DE3;
RX PubMed=16079137; DOI=10.1074/jbc.M506479200;
RA Stenberg F., Chovanec P., Maslen S.L., Robinson C.V., Ilag L.,
RA von Heijne G., Daley D.O.;
RT "Protein complexes of the Escherichia coli cell envelope.";
RL J. Biol. Chem. 280:34409-34419(2005).
RN [7]
RP FUNCTION, SUBUNIT, INTERACTION WITH BAMA AND BAMC, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=K12;
RX PubMed=16824102; DOI=10.1111/j.1365-2958.2006.05211.x;
RA Malinverni J.C., Werner J., Kim S., Sklar J.G., Kahne D., Misra R.,
RA Silhavy T.J.;
RT "YfiO stabilizes the YaeT complex and is essential for outer membrane
RT protein assembly in Escherichia coli.";
RL Mol. Microbiol. 61:151-164(2006).
RN [8]
RP FUNCTION, AND SUBUNIT.
RX PubMed=20378773; DOI=10.1126/science.1188919;
RA Hagan C.L., Kim S., Kahne D.;
RT "Reconstitution of outer membrane protein assembly from purified
RT components.";
RL Science 328:890-892(2010).
RN [9]
RP FUNCTION, AND SUBUNIT.
RX PubMed=21823654; DOI=10.1021/bi2010784;
RA Hagan C.L., Kahne D.;
RT "The reconstituted Escherichia coli Bam complex catalyzes multiple
RT rounds of beta-barrel assembly.";
RL Biochemistry 50:7444-7446(2011).
RN [10]
RP CRYSTALLIZATION.
RX PubMed=21139201; DOI=10.1107/S1744309110034160;
RA Albrecht R., Zeth K.;
RT "Crystallization and preliminary X-ray data collection of the
RT Escherichia coli lipoproteins BamC, BamD and BamE.";
RL Acta Crystallogr. F 66:1586-1590(2010).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 29-245, INTERACTION WITH
RP BAMA, SUBUNIT, AND FUNCTION.
RX PubMed=21586578; DOI=10.1074/jbc.M111.238931;
RA Albrecht R., Zeth K.;
RT "Structural basis of outer membrane protein biogenesis in bacteria.";
RL J. Biol. Chem. 286:27792-27803(2011).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.90 ANGSTROMS) OF 21-245, AND INTERACTION WITH
RP BAMC.
RC STRAIN=K12;
RX PubMed=21937441; DOI=10.1074/jbc.M111.298166;
RA Kim K.H., Aulakh S., Paetzel M.;
RT "Crystal structure of beta-barrel assembly machinery BamCD protein
RT complex.";
RL J. Biol. Chem. 286:39116-39121(2011).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 23-245, FUNCTION, SUBUNIT,
RP AND DOMAIN.
RX PubMed=22281737; DOI=10.1107/S0907444911051031;
RA Dong C., Hou H., Yang X., Dong Y., Shen Y.;
RT "Structure of Escherichia coli BamD and its functional implications in
RT outer membrane protein assembly.";
RL Acta Crystallogr. D 68:95-101(2012).
CC -!- FUNCTION: Part of the outer membrane protein assembly complex,
CC which is involved in assembly and insertion of beta-barrel
CC proteins into the outer membrane. Constitutes, with BamA, the core
CC component of the assembly machinery. Probably involved in
CC transient protein interactions. {ECO:0000255|HAMAP-Rule:MF_00922,
CC ECO:0000269|PubMed:16824102, ECO:0000269|PubMed:20378773,
CC ECO:0000269|PubMed:21586578, ECO:0000269|PubMed:21823654,
CC ECO:0000269|PubMed:22281737}.
CC -!- SUBUNIT: Part of the Bam complex, which is composed of the outer
CC membrane protein BamA, and four lipoproteins BamB, BamC, BamD and
CC BamE. Forms a subcomplex with BamC and BamE. Interacts directly
CC with BamA. {ECO:0000255|HAMAP-Rule:MF_00922,
CC ECO:0000269|PubMed:15851030, ECO:0000269|PubMed:16079137,
CC ECO:0000269|PubMed:16824102, ECO:0000269|PubMed:20378773,
CC ECO:0000269|PubMed:21586578, ECO:0000269|PubMed:21823654,
CC ECO:0000269|PubMed:21937441, ECO:0000269|PubMed:22281737}.
CC -!- INTERACTION:
CC P76459:atoA; NbExp=2; IntAct=EBI-1128087, EBI-1128061;
CC P0A940:bamA; NbExp=13; IntAct=EBI-1128087, EBI-907371;
CC P0A903:bamC; NbExp=4; IntAct=EBI-1128087, EBI-1129043;
CC -!- SUBCELLULAR LOCATION: Cell outer membrane {ECO:0000255|HAMAP-
CC Rule:MF_00922, ECO:0000269|PubMed:16079137}; Lipid-anchor
CC {ECO:0000255|HAMAP-Rule:MF_00922, ECO:0000269|PubMed:16079137}.
CC -!- DOMAIN: The N-terminal may interact with various proteins as a
CC chaperone to assist in the folding and insertion of proteins into
CC the outer membrane. The C-terminal region may serve as the link
CC between BamA, BamC and BamE. {ECO:0000269|PubMed:22281737}.
CC -!- DISRUPTION PHENOTYPE: Depletion decreases the density of outer
CC membrane proteins, but does not significantly affect transport of
CC lipopolysaccharides to the outer membrane.
CC {ECO:0000269|PubMed:16824102}.
CC -!- SIMILARITY: Belongs to the BamD family. {ECO:0000255|HAMAP-
CC Rule:MF_00922}.
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DR EMBL; U00096; AAC75644.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16480.1; -; Genomic_DNA.
DR EMBL; Z70523; CAA94434.1; -; Genomic_DNA.
DR PIR; F65037; F65037.
DR RefSeq; NP_417086.1; NC_000913.3.
DR RefSeq; WP_000197686.1; NZ_LN832404.1.
DR PDB; 2YHC; X-ray; 1.80 A; A=29-245.
DR PDB; 3Q5M; X-ray; 2.60 A; A=23-245.
DR PDB; 3TGO; X-ray; 2.90 A; A/B=21-245.
DR PDB; 5AYW; X-ray; 3.56 A; D=20-245.
DR PDB; 5D0O; X-ray; 2.90 A; D=1-245.
DR PDB; 5D0Q; X-ray; 3.50 A; D/H=1-245.
DR PDB; 5EKQ; X-ray; 3.39 A; D=20-245.
DR PDBsum; 2YHC; -.
DR PDBsum; 3Q5M; -.
DR PDBsum; 3TGO; -.
DR PDBsum; 5AYW; -.
DR PDBsum; 5D0O; -.
DR PDBsum; 5D0Q; -.
DR PDBsum; 5EKQ; -.
DR ProteinModelPortal; P0AC02; -.
DR SMR; P0AC02; -.
DR BioGrid; 4260615; 263.
DR BioGrid; 851422; 1.
DR DIP; DIP-51120N; -.
DR IntAct; P0AC02; 6.
DR MINT; MINT-8141303; -.
DR STRING; 511145.b2595; -.
DR TCDB; 1.B.33.1.3; the outer membrane protein insertion porin (bam complex) (ompip) family.
DR EPD; P0AC02; -.
DR PaxDb; P0AC02; -.
DR PRIDE; P0AC02; -.
DR EnsemblBacteria; AAC75644; AAC75644; b2595.
DR EnsemblBacteria; BAA16480; BAA16480; BAA16480.
DR GeneID; 947086; -.
DR KEGG; ecj:JW2577; -.
DR KEGG; eco:b2595; -.
DR PATRIC; 32120593; VBIEscCol129921_2695.
DR EchoBASE; EB3974; -.
DR EcoGene; EG14222; bamD.
DR eggNOG; ENOG4106SNF; Bacteria.
DR eggNOG; COG4105; LUCA.
DR HOGENOM; HOG000260923; -.
DR InParanoid; P0AC02; -.
DR KO; K05807; -.
DR OMA; IHVADYY; -.
DR PhylomeDB; P0AC02; -.
DR BioCyc; EcoCyc:G7352-MONOMER; -.
DR PRO; PR:P0AC02; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:1990063; C:Bam protein complex; IDA:EcoCyc.
DR GO; GO:0043165; P:Gram-negative-bacterium-type cell outer membrane assembly; IDA:EcoCyc.
DR GO; GO:0051205; P:protein insertion into membrane; IDA:EcoCyc.
DR CDD; cd15830; BamD; 1.
DR HAMAP; MF_00922; OM_assembly_BamD; 1.
DR InterPro; IPR017689; BamD.
DR InterPro; IPR011990; TPR-like_helical_dom.
DR SUPFAM; SSF48452; SSF48452; 1.
DR TIGRFAMs; TIGR03302; OM_YfiO; 1.
DR PROSITE; PS51257; PROKAR_LIPOPROTEIN; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell outer membrane; Complete proteome; Lipoprotein;
KW Membrane; Palmitate; Reference proteome; Signal.
FT SIGNAL 1 19 {ECO:0000255|HAMAP-Rule:MF_00922}.
FT CHAIN 20 245 Outer membrane protein assembly factor
FT BamD.
FT /FTId=PRO_0000036226.
FT LIPID 20 20 N-palmitoyl cysteine. {ECO:0000305}.
FT LIPID 20 20 S-diacylglycerol cysteine. {ECO:0000305}.
FT CONFLICT 59 59 D -> Y (in Ref. 4; CAA94434).
FT {ECO:0000305}.
FT HELIX 32 45 {ECO:0000244|PDB:2YHC}.
FT HELIX 48 61 {ECO:0000244|PDB:2YHC}.
FT HELIX 68 81 {ECO:0000244|PDB:2YHC}.
FT HELIX 85 98 {ECO:0000244|PDB:2YHC}.
FT STRAND 100 102 {ECO:0000244|PDB:5D0O}.
FT HELIX 105 120 {ECO:0000244|PDB:2YHC}.
FT TURN 126 129 {ECO:0000244|PDB:3TGO}.
FT STRAND 133 135 {ECO:0000244|PDB:5D0Q}.
FT HELIX 138 151 {ECO:0000244|PDB:2YHC}.
FT HELIX 160 188 {ECO:0000244|PDB:2YHC}.
FT HELIX 191 204 {ECO:0000244|PDB:2YHC}.
FT HELIX 209 224 {ECO:0000244|PDB:2YHC}.
FT HELIX 228 240 {ECO:0000244|PDB:2YHC}.
CC --------------------------------------------------------------------------
CC The following FT lines are automated annotations from the MyHits database.
CC --------------------------------------------------------------------------
FT MYHIT 4 242 ihamap:OM_assembly_BamD [T]
SQ SEQUENCE 245 AA; 27829 MW; 91D0A25E69248C49 CRC64;
MTRMKYLVAA ATLSLFLAGC SGSKEEVPDN PPNEIYATAQ QKLQDGNWRQ AITQLEALDN
RYPFGPYSQQ VQLDLIYAYY KNADLPLAQA AIDRFIRLNP THPNIDYVMY MRGLTNMALD
DSALQGFFGV DRSDRDPQHA RAAFSDFSKL VRGYPNSQYT TDATKRLVFL KDRLAKYEYS
VAEYYTERGA WVAVVNRVEG MLRDYPDTQA TRDALPLMEN AYRQMQMNAQ AEKVAKIIAA
NSSNT
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