BAMD_ECOLI
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 03-AUG-2022, entry version 127.
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., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT 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., Mau B.,
RA 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 MG1655
RT 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 in
RT 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 membrane
RT 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 rounds
RT 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 Escherichia
RT coli lipoproteins BamC, BamD and BamE.";
RL Acta Crystallogr. F 66:1586-1590(2010).
RN [11] {ECO:0007744|PDB:2YHC}
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 29-245, INTERACTION WITH BAMA,
RP 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] {ECO:0007744|PDB:3TGO}
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] {ECO:0007744|PDB:3Q5M}
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 23-245, FUNCTION, SUBUNIT, AND
RP 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).
RN [14] {ECO:0007744|PDB:5LJO}
RP STRUCTURE BY ELECTRON MICROSCOPY (4.90 ANGSTROMS) OF 26-243 IN LATERAL OPEN
RP BAM COMPLEX, FUNCTION, SUBUNIT, MASS SPECTROMETRY, DIACYLGLYCEROL AT
RP CYS-20, AND PALMITOYLATION AT CYS-20.
RX PubMed=27686148; DOI=10.1038/ncomms12865;
RA Iadanza M.G., Higgins A.J., Schiffrin B., Calabrese A.N., Brockwell D.J.,
RA Ashcroft A.E., Radford S.E., Ranson N.A.;
RT "Lateral opening in the intact beta-barrel assembly machinery captured by
RT cryo-EM.";
RL Nat. Commun. 7:12865-12865(2016).
RN [15] {ECO:0007744|PDB:5AYW}
RP X-RAY CRYSTALLOGRAPHY (3.56 ANGSTROMS) OF 20-245 IN LATERAL CLOSED BAM
RP COMPLEX, SUBUNIT, AND SUBCELLULAR LOCATION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=26900875; DOI=10.1038/nsmb.3181;
RA Han L., Zheng J., Wang Y., Yang X., Liu Y., Sun C., Cao B., Zhou H., Ni D.,
RA Lou J., Zhao Y., Huang Y.;
RT "Structure of the BAM complex and its implications for biogenesis of outer-
RT membrane proteins.";
RL Nat. Struct. Mol. Biol. 23:192-196(2016).
RN [16] {ECO:0007744|PDB:5D0O, ECO:0007744|PDB:5D0Q}
RP X-RAY CRYSTALLOGRAPHY (2.90 ANGSTROMS) IN LATERAL CLOSED BAM COMPLEX AND
RP LATERAL OPEN BAMACDE SUBCOMPLEX, SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=26901871; DOI=10.1038/nature17199;
RA Gu Y., Li H., Dong H., Zeng Y., Zhang Z., Paterson N.G., Stansfeld P.J.,
RA Wang Z., Zhang Y., Wang W., Dong C.;
RT "Structural basis of outer membrane protein insertion by the BAM complex.";
RL Nature 531:64-69(2016).
RN [17] {ECO:0007744|PDB:5EKQ}
RP X-RAY CRYSTALLOGRAPHY (3.39 ANGSTROMS) OF 20-245 OF LATERAL OPEN BAMACDE
RP COMPLEX, AND SUBUNIT.
RX PubMed=26744406; DOI=10.1126/science.aad3460;
RA Bakelar J., Buchanan S.K., Noinaj N.;
RT "The structure of the beta-barrel assembly machinery complex.";
RL Science 351:180-186(2016).
CC -!- FUNCTION: Part of the outer membrane protein assembly complex (Bam),
CC which is involved in assembly and insertion of beta-barrel proteins
CC into the outer membrane. Constitutes, with BamA, the core component of
CC the assembly machinery. Probably involved in transient protein
CC interactions. Efficient substrate folding and insertion into the outer
CC membrane requires all 5 subunits (PubMed:20378773, PubMed:21823654,
CC PubMed:27686148). A lateral gate may open between the first and last
CC strands of the BamA beta-barrel that allows substrate to insert into
CC the outer membrane; comparison of the structures of complete and nearly
CC complete Bam complexes show there is considerable movement of all 5
CC proteins (PubMed:27686148, PubMed:26900875, PubMed:26901871,
CC PubMed:26744406). {ECO:0000269|PubMed:16824102,
CC ECO:0000269|PubMed:20378773, ECO:0000269|PubMed:21586578,
CC ECO:0000269|PubMed:21823654, ECO:0000269|PubMed:22281737,
CC ECO:0000269|PubMed:26744406, ECO:0000269|PubMed:26900875,
CC ECO:0000269|PubMed:26901871, ECO:0000269|PubMed:27686148}.
CC -!- SUBUNIT: Part of the Bam complex, which is composed of the outer
CC membrane protein BamA, and four lipoproteins BamB, BamC, BamD and BamE.
CC Forms a subcomplex with BamC and BamE. Interacts directly with BamA.
CC The Bam complex has the shape of a hat, with the BamA beta-barrel crown
CC in the outer membrane and the periplasmic brim formed by the BamA POTRA
CC domains and the 4 lipoproteins (PubMed:27686148, PubMed:26900875,
CC PubMed:26901871, PubMed:26744406). {ECO:0000269|PubMed:15851030,
CC ECO:0000269|PubMed:16079137, ECO:0000269|PubMed:16824102,
CC ECO:0000269|PubMed:20378773, ECO:0000269|PubMed:21586578,
CC ECO:0000269|PubMed:21823654, ECO:0000269|PubMed:21937441,
CC ECO:0000269|PubMed:22281737, ECO:0000269|PubMed:26744406,
CC ECO:0000269|PubMed:26900875, ECO:0000269|PubMed:26901871,
CC ECO:0000269|PubMed:27686148}.
CC -!- INTERACTION:
CC P0AC02; P76459: atoA; NbExp=2; IntAct=EBI-1128087, EBI-1128061;
CC P0AC02; P0A940: bamA; NbExp=26; IntAct=EBI-1128087, EBI-907371;
CC P0AC02; P0A903: bamC; NbExp=4; IntAct=EBI-1128087, EBI-1129043;
CC P0AC02; P0A937: bamE; NbExp=3; IntAct=EBI-1128087, EBI-6391574;
CC -!- SUBCELLULAR LOCATION: Cell outer membrane {ECO:0000255|HAMAP-
CC Rule:MF_00922, ECO:0000269|PubMed:16079137,
CC ECO:0000269|PubMed:26900875, ECO:0000269|PubMed:26901871}; Lipid-anchor
CC {ECO:0000255|HAMAP-Rule:MF_00922, ECO:0000269|PubMed:16079137,
CC ECO:0000269|PubMed:27686148}.
CC -!- DOMAIN: The N-terminal may interact with various proteins as a
CC chaperone to assist in the folding and insertion of proteins into the
CC outer membrane. The C-terminal region may serve as the link between
CC BamA, BamC and BamE. {ECO:0000269|PubMed:22281737}.
CC -!- MASS SPECTROMETRY: Mass=26582; Method=Electrospray; Note=With 3
CC palmitic acid (C16) acyl chains.;
CC Evidence={ECO:0000269|PubMed:27686148};
CC -!- MASS SPECTROMETRY: Mass=26603; Method=Electrospray; Note=With 2
CC palmitic (C16) and 1 stearic (C18) acid acyl chains.;
CC Evidence={ECO:0000269|PubMed:27686148};
CC -!- DISRUPTION PHENOTYPE: Depletion decreases the density of outer membrane
CC 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_STEB01000040.1.
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 PDB; 5LJO; EM; 4.90 A; D=26-243.
DR PDB; 6LYQ; X-ray; 3.19 A; D=1-245.
DR PDB; 6LYR; X-ray; 3.28 A; D=1-245.
DR PDB; 6LYS; X-ray; 3.05 A; D=1-245.
DR PDB; 6LYU; EM; 4.20 A; D=1-245.
DR PDB; 6SMX; EM; 6.65 A; D=26-243.
DR PDB; 6SN0; EM; 10.80 A; D=26-243.
DR PDB; 6SN2; EM; 9.50 A; D=26-243.
DR PDB; 6SN3; EM; 8.40 A; D=26-243.
DR PDB; 6SN4; EM; 9.50 A; D=26-243.
DR PDB; 6SN5; EM; 9.80 A; D=26-243.
DR PDB; 6SN7; EM; 8.90 A; D=26-243.
DR PDB; 6SN8; EM; 8.40 A; D=26-243.
DR PDB; 6SN9; EM; 9.80 A; D=26-243.
DR PDB; 6SO7; EM; 10.50 A; D=26-243.
DR PDB; 6SO8; EM; 9.80 A; D=26-243.
DR PDB; 6SOA; EM; 10.80 A; D=26-243.
DR PDB; 6SOB; EM; 8.50 A; D=26-243.
DR PDB; 6SOC; EM; 9.00 A; D=26-243.
DR PDB; 6SOG; EM; 8.30 A; D=26-243.
DR PDB; 6SOH; EM; 9.50 A; D=26-243.
DR PDB; 6SOJ; EM; 10.40 A; D=26-243.
DR PDB; 6V05; EM; 4.10 A; D=1-245.
DR PDB; 7BNQ; EM; 4.10 A; D=1-245.
DR PDB; 7NBX; EM; 4.80 A; D=1-245.
DR PDB; 7NCS; EM; 7.10 A; D=1-245.
DR PDB; 7ND0; EM; 5.20 A; D=1-245.
DR PDB; 7NRI; EM; 3.03 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 PDBsum; 5LJO; -.
DR PDBsum; 6LYQ; -.
DR PDBsum; 6LYR; -.
DR PDBsum; 6LYS; -.
DR PDBsum; 6LYU; -.
DR PDBsum; 6SMX; -.
DR PDBsum; 6SN0; -.
DR PDBsum; 6SN2; -.
DR PDBsum; 6SN3; -.
DR PDBsum; 6SN4; -.
DR PDBsum; 6SN5; -.
DR PDBsum; 6SN7; -.
DR PDBsum; 6SN8; -.
DR PDBsum; 6SN9; -.
DR PDBsum; 6SO7; -.
DR PDBsum; 6SO8; -.
DR PDBsum; 6SOA; -.
DR PDBsum; 6SOB; -.
DR PDBsum; 6SOC; -.
DR PDBsum; 6SOG; -.
DR PDBsum; 6SOH; -.
DR PDBsum; 6SOJ; -.
DR PDBsum; 6V05; -.
DR PDBsum; 7BNQ; -.
DR PDBsum; 7NBX; -.
DR PDBsum; 7NCS; -.
DR PDBsum; 7ND0; -.
DR PDBsum; 7NRI; -.
DR AlphaFoldDB; P0AC02; -.
DR SMR; P0AC02; -.
DR BioGRID; 4260615; 311.
DR BioGRID; 851422; 3.
DR ComplexPortal; CPX-1923; BAM complex.
DR DIP; DIP-51120N; -.
DR IntAct; P0AC02; 6.
DR MINT; P0AC02; -.
DR STRING; 511145.b2595; -.
DR TCDB; 1.B.33.1.3; the outer membrane protein insertion porin (bam complex) (ompip) family.
DR jPOST; P0AC02; -.
DR PaxDb; P0AC02; -.
DR PRIDE; P0AC02; -.
DR EnsemblBacteria; AAC75644; AAC75644; b2595.
DR EnsemblBacteria; BAA16480; BAA16480; BAA16480.
DR GeneID; 67414086; -.
DR GeneID; 947086; -.
DR KEGG; ecj:JW2577; -.
DR KEGG; eco:b2595; -.
DR PATRIC; fig|1411691.4.peg.4142; -.
DR EchoBASE; EB3974; -.
DR eggNOG; COG4105; Bacteria.
DR HOGENOM; CLU_065982_0_2_6; -.
DR InParanoid; P0AC02; -.
DR OMA; VERQHPY; -.
DR PhylomeDB; P0AC02; -.
DR BioCyc; EcoCyc:G7352-MON; -.
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:0009279; C:cell outer membrane; IDA:EcoCyc.
DR GO; GO:0016020; C:membrane; IDA:ComplexPortal.
DR GO; GO:0043165; P:Gram-negative-bacterium-type cell outer membrane assembly; IDA:ComplexPortal.
DR GO; GO:0051205; P:protein insertion into membrane; IDA:ComplexPortal.
DR CDD; cd15830; BamD; 1.
DR Gene3D; 1.25.40.10; -; 1.
DR HAMAP; MF_00922; OM_assembly_BamD; 1.
DR InterPro; IPR017689; BamD.
DR InterPro; IPR039565; BamD-like.
DR InterPro; IPR011990; TPR-like_helical_dom_sf.
DR Pfam; PF13525; YfiO; 1.
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; Lipoprotein; Membrane; Palmitate;
KW Reference proteome; Signal.
FT SIGNAL 1..19
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00922"
FT CHAIN 20..245
FT /note="Outer membrane protein assembly factor BamD"
FT /id="PRO_0000036226"
FT LIPID 20
FT /note="N-palmitoyl cysteine"
FT /evidence="ECO:0000305|PubMed:27686148"
FT LIPID 20
FT /note="S-diacylglycerol cysteine"
FT /evidence="ECO:0000305|PubMed:27686148"
FT CONFLICT 59
FT /note="D -> Y (in Ref. 4; CAA94434)"
FT /evidence="ECO:0000305"
FT HELIX 32..45
FT /evidence="ECO:0007829|PDB:2YHC"
FT HELIX 48..61
FT /evidence="ECO:0007829|PDB:2YHC"
FT STRAND 63..65
FT /evidence="ECO:0007829|PDB:6LYS"
FT HELIX 68..81
FT /evidence="ECO:0007829|PDB:2YHC"
FT HELIX 85..98
FT /evidence="ECO:0007829|PDB:2YHC"
FT STRAND 100..102
FT /evidence="ECO:0007829|PDB:5D0O"
FT HELIX 105..120
FT /evidence="ECO:0007829|PDB:2YHC"
FT TURN 126..129
FT /evidence="ECO:0007829|PDB:3TGO"
FT STRAND 133..135
FT /evidence="ECO:0007829|PDB:5D0Q"
FT HELIX 138..151
FT /evidence="ECO:0007829|PDB:2YHC"
FT HELIX 160..188
FT /evidence="ECO:0007829|PDB:2YHC"
FT HELIX 191..204
FT /evidence="ECO:0007829|PDB:2YHC"
FT STRAND 205..208
FT /evidence="ECO:0007829|PDB:6LYQ"
FT HELIX 209..224
FT /evidence="ECO:0007829|PDB:2YHC"
FT HELIX 228..240
FT /evidence="ECO:0007829|PDB:2YHC"
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
