AIDB_ECOLI
ID AIDB_ECOLI Reviewed; 541 AA.
AC P33224; P33223; Q2M6B8;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2000, sequence version 3.
DT 03-AUG-2022, entry version 165.
DE RecName: Full=Putative acyl-CoA dehydrogenase AidB;
DE EC=1.3.99.-;
GN Name=aidB; OrderedLocusNames=b4187, JW5867;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND INDUCTION.
RC STRAIN=K12 / MV1161;
RX PubMed=7961409; DOI=10.1128/jb.176.21.6583-6589.1994;
RA Landini P., Hajec L.I., Volkert M.R.;
RT "Structure and transcriptional regulation of the Escherichia coli adaptive
RT response gene aidB.";
RL J. Bacteriol. 176:6583-6589(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7610040; DOI=10.1093/nar/23.12.2105;
RA Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.;
RT "Analysis of the Escherichia coli genome VI: DNA sequence of the region
RT from 92.8 through 100 minutes.";
RL Nucleic Acids Res. 23:2105-2119(1995).
RN [3]
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 [4]
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 [5]
RP PROTEIN SEQUENCE OF 195-204, FUNCTION, DNA-BINDING, COFACTOR, AND SUBUNIT.
RC STRAIN=K12;
RX PubMed=16352838; DOI=10.1128/jb.188.1.223-230.2006;
RA Rohankhedkar M.S., Mulrooney S.B., Wedemeyer W.J., Hausinger R.P.;
RT "The AidB component of the Escherichia coli adaptive response to alkylating
RT agents is a flavin-containing, DNA-binding protein.";
RL J. Bacteriol. 188:223-230(2006).
RN [6]
RP DNA-BINDING, DOMAIN, AUTOREGULATION, AND INDUCTION.
RC STRAIN=K12;
RX PubMed=20889740; DOI=10.1128/jb.00858-10;
RA Rippa V., Amoresano A., Esposito C., Landini P., Volkert M., Duilio A.;
RT "Specific DNA binding and regulation of its own expression by the AidB
RT protein in Escherichia coli.";
RL J. Bacteriol. 192:6136-6142(2010).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH FAD, FUNCTION,
RP COFACTOR, SUBUNIT, AND MUTAGENESIS OF ARG-437 AND ARG-518.
RX PubMed=18829440; DOI=10.1073/pnas.0806521105;
RA Bowles T., Metz A.H., O'Quin J., Wawrzak Z., Eichman B.F.;
RT "Structure and DNA binding of alkylation response protein AidB.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:15299-15304(2008).
CC -!- FUNCTION: Part of the adaptive DNA-repair response to alkylating
CC agents. Could prevent alkylation damage by protecting DNA and
CC destroying alkylating agents that have yet to reach their DNA target.
CC Binds to double-stranded DNA with a preference for a DNA region that
CC includes its own promoter. Shows weak isovaleryl-CoA dehydrogenase
CC activity in vitro. {ECO:0000269|PubMed:16352838,
CC ECO:0000269|PubMed:18829440, ECO:0000269|PubMed:7961409}.
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC -!- SUBUNIT: Homotetramer. Dimer of dimers. {ECO:0000269|PubMed:16352838,
CC ECO:0000269|PubMed:18829440}.
CC -!- INTERACTION:
CC P33224; P33224: aidB; NbExp=3; IntAct=EBI-542726, EBI-542726;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- INDUCTION: Regulated by Ada in response to alkylating agents. Also
CC induced by anaerobiosis or by acetate at pH 6.5, via RpoS. Represses
CC its own synthesis during normal cell growth.
CC {ECO:0000269|PubMed:20889740, ECO:0000269|PubMed:7961409}.
CC -!- DOMAIN: The N-terminal region contains FAD-dependent dehydrogenase
CC activity and the C-terminal region contains DNA-binding activity.
CC {ECO:0000269|PubMed:20889740}.
CC -!- SIMILARITY: Belongs to the acyl-CoA dehydrogenase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA97083.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAC18889.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; L20915; AAC18889.1; ALT_INIT; Genomic_DNA.
DR EMBL; L20915; AAC18890.1; -; Genomic_DNA.
DR EMBL; U14003; AAA97083.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC77144.2; -; Genomic_DNA.
DR EMBL; AP009048; BAE78188.1; -; Genomic_DNA.
DR PIR; I41124; I41124.
DR RefSeq; NP_418608.6; NC_000913.3.
DR RefSeq; WP_001350567.1; NZ_LN832404.1.
DR PDB; 3DJL; X-ray; 1.70 A; A=1-541.
DR PDB; 3U33; X-ray; 2.80 A; A/B/C/D/E/F/G/H/I/J/K/L=1-541.
DR PDBsum; 3DJL; -.
DR PDBsum; 3U33; -.
DR AlphaFoldDB; P33224; -.
DR SMR; P33224; -.
DR BioGRID; 4262695; 240.
DR DIP; DIP-9078N; -.
DR IntAct; P33224; 32.
DR STRING; 511145.b4187; -.
DR jPOST; P33224; -.
DR PaxDb; P33224; -.
DR PRIDE; P33224; -.
DR EnsemblBacteria; AAC77144; AAC77144; b4187.
DR EnsemblBacteria; BAE78188; BAE78188; BAE78188.
DR GeneID; 948710; -.
DR KEGG; ecj:JW5867; -.
DR KEGG; eco:b4187; -.
DR PATRIC; fig|1411691.4.peg.2514; -.
DR EchoBASE; EB1759; -.
DR eggNOG; COG1960; Bacteria.
DR HOGENOM; CLU_016513_0_0_6; -.
DR InParanoid; P33224; -.
DR OMA; GNVQCLD; -.
DR PhylomeDB; P33224; -.
DR BioCyc; EcoCyc:EG11811-MON; -.
DR BioCyc; MetaCyc:EG11811-MON; -.
DR EvolutionaryTrace; P33224; -.
DR PRO; PR:P33224; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0008470; F:isovaleryl-CoA dehydrogenase activity; IDA:EcoCyc.
DR GO; GO:0043565; F:sequence-specific DNA binding; IDA:EcoCyc.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IEP:EcoCyc.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IDA:EcoCyc.
DR CDD; cd01154; AidB; 1.
DR InterPro; IPR006089; Acyl-CoA_DH_CS.
DR InterPro; IPR006091; Acyl-CoA_Oxase/DH_mid-dom.
DR InterPro; IPR036250; AcylCo_DH-like_C.
DR InterPro; IPR009075; AcylCo_DH/oxidase_C.
DR InterPro; IPR009100; AcylCoA_DH/oxidase_NM_dom.
DR InterPro; IPR034184; AidB.
DR InterPro; IPR041504; AidB_N.
DR Pfam; PF00441; Acyl-CoA_dh_1; 1.
DR Pfam; PF02770; Acyl-CoA_dh_M; 1.
DR Pfam; PF18158; AidB_N; 1.
DR SUPFAM; SSF47203; SSF47203; 1.
DR SUPFAM; SSF56645; SSF56645; 1.
DR PROSITE; PS00072; ACYL_COA_DH_1; 1.
DR PROSITE; PS00073; ACYL_COA_DH_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; DNA-binding; FAD;
KW Flavoprotein; Oxidoreductase; Reference proteome; Stress response.
FT CHAIN 1..541
FT /note="Putative acyl-CoA dehydrogenase AidB"
FT /id="PRO_0000201192"
FT REGION 445..541
FT /note="dsDNA-binding"
FT BINDING 182..191
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:18829440"
FT BINDING 185
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:18829440"
FT BINDING 191
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:18829440"
FT BINDING 216..218
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:18829440"
FT BINDING 218
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:18829440"
FT BINDING 423..433
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:18829440"
FT BINDING 429
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:18829440"
FT MUTAGEN 437
FT /note="R->Q: Does not affect DNA binding affinity."
FT /evidence="ECO:0000269|PubMed:18829440"
FT MUTAGEN 518
FT /note="R->Q: Reduces DNA binding affinity."
FT /evidence="ECO:0000269|PubMed:18829440"
FT TURN 20..23
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 25..33
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 37..39
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 40..50
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 53..64
FT /evidence="ECO:0007829|PDB:3DJL"
FT STRAND 68..72
FT /evidence="ECO:0007829|PDB:3DJL"
FT STRAND 78..83
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 86..97
FT /evidence="ECO:0007829|PDB:3DJL"
FT TURN 98..102
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 103..105
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 113..127
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 132..148
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 151..156
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 157..160
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 172..174
FT /evidence="ECO:0007829|PDB:3DJL"
FT STRAND 175..177
FT /evidence="ECO:0007829|PDB:3DJL"
FT STRAND 180..183
FT /evidence="ECO:0007829|PDB:3DJL"
FT STRAND 189..191
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 193..195
FT /evidence="ECO:0007829|PDB:3DJL"
FT STRAND 199..202
FT /evidence="ECO:0007829|PDB:3DJL"
FT STRAND 208..218
FT /evidence="ECO:0007829|PDB:3DJL"
FT STRAND 222..231
FT /evidence="ECO:0007829|PDB:3DJL"
FT STRAND 234..243
FT /evidence="ECO:0007829|PDB:3DJL"
FT STRAND 251..257
FT /evidence="ECO:0007829|PDB:3DJL"
FT STRAND 260..262
FT /evidence="ECO:0007829|PDB:3U33"
FT STRAND 268..283
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 287..290
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 292..323
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 331..333
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 335..363
FT /evidence="ECO:0007829|PDB:3DJL"
FT TURN 364..366
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 368..400
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 401..405
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 411..423
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 424..426
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 427..441
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 445..454
FT /evidence="ECO:0007829|PDB:3DJL"
FT TURN 455..458
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 461..473
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 479..481
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 482..501
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 504..515
FT /evidence="ECO:0007829|PDB:3DJL"
FT HELIX 525..534
FT /evidence="ECO:0007829|PDB:3DJL"
SQ SEQUENCE 541 AA; 60590 MW; D609E364E3A99208 CRC64;
MHWQTHTVFN QPIPLNNSNL YLSDGALCEA VTREGAGWDS DFLASIGQQL GTAESLELGR
LANVNPPELL RYDAQGRRLD DVRFHPAWHL LMQALCTNRV HNLAWEEDAR SGAFVARAAR
FMLHAQVEAG SLCPITMTFA ATPLLLQMLP APFQDWTTPL LSDRYDSHLL PGGQKRGLLI
GMGMTEKQGG SDVMSNTTRA ERLEDGSYRL VGHKWFFSVP QSDAHLVLAQ TAGGLSCFFV
PRFLPDGQRN AIRLERLKDK LGNRSNASCE VEFQDAIGWL LGLEGEGIRL ILKMGGMTRF
DCALGSHAMM RRAFSLAIYH AHQRHVFGNP LIQQPLMRHV LSRMALQLEG QTALLFRLAR
AWDRRADAKE ALWARLFTPA AKFVICKRGM PFVAEAMEVL GGIGYCEESE LPRLYREMPV
NSIWEGSGNI MCLDVLRVLN KQAGVYDLLS EAFVEVKGQD RYFDRAVRRL QQQLRKPAEE
LGREITHQLF LLGCGAQMLK YASPPMAQAW CQVMLDTRGG VRLSEQIQND LLLRATGGVC
V
