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Bifunctional ligase/repressor BirA (Biotin operon repressor) (Biotin--[acetyl-CoA-carboxylase] ligase) (EC 6.3.4.15) (Biotin--protein ligase) (Biotin-[acetyl-CoA carboxylase] synthetase)

 BIRA_ECOLI              Reviewed;         321 AA.
P06709; Q2M8R4;
01-JAN-1988, integrated into UniProtKB/Swiss-Prot.
01-JAN-1988, sequence version 1.
27-SEP-2017, entry version 167.
RecName: Full=Bifunctional ligase/repressor BirA {ECO:0000255|HAMAP-Rule:MF_00978};
AltName: Full=Biotin operon repressor {ECO:0000255|HAMAP-Rule:MF_00978};
AltName: Full=Biotin--[acetyl-CoA-carboxylase] ligase {ECO:0000255|HAMAP-Rule:MF_00978};
EC=6.3.4.15 {ECO:0000255|HAMAP-Rule:MF_00978};
AltName: Full=Biotin--protein ligase {ECO:0000255|HAMAP-Rule:MF_00978};
AltName: Full=Biotin-[acetyl-CoA carboxylase] synthetase {ECO:0000255|HAMAP-Rule:MF_00978};
Name=birA {ECO:0000255|HAMAP-Rule:MF_00978}; Synonyms=bioR, dhbB;
OrderedLocusNames=b3973, JW3941;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=3899863; DOI=10.1016/0378-1119(85)90011-3;
Howard P.K., Shaw J., Otsuka A.J.;
"Nucleotide sequence of the birA gene encoding the biotin operon
repressor and biotin holoenzyme synthetase functions of Escherichia
coli.";
Gene 35:321-331(1985).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=3536662; DOI=10.1016/0378-1119(86)90189-7;
Buoncristiani M.R., Howard P.K., Otsuka A.J.;
"DNA-binding and enzymatic domains of the bifunctional biotin operon
repressor (BirA) of Escherichia coli.";
Gene 44:255-261(1986).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=8265357; DOI=10.1093/nar/21.23.5408;
Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J.,
Daniels D.L.;
"Analysis of the Escherichia coli genome. IV. DNA sequence of the
region from 89.2 to 92.8 minutes.";
Nucleic Acids Res. 21:5408-5417(1993).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[6]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-76.
STRAIN=RDD012;
PubMed=1311302; DOI=10.1128/jb.174.5.1690-1693.1992;
Pucci M.J., Discotto L.F., Dougherty T.J.;
"Cloning and identification of the Escherichia coli murB DNA sequence,
which encodes UDP-N-acetylenolpyruvoylglucosamine reductase.";
J. Bacteriol. 174:1690-1693(1992).
[7]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 226-321.
PubMed=1328157; DOI=10.1128/jb.174.20.6411-6417.1992;
Song W.-J., Jackowski S.;
"Cloning, sequencing, and expression of the pantothenate kinase (coaA)
gene of Escherichia coli.";
J. Bacteriol. 174:6411-6417(1992).
[8]
FUNCTION, CATALYTIC ACTIVITY, AND SUBUNIT.
PubMed=6129246;
Eisenberg M.A., Prakash O., Hsiung S.C.;
"Purification and properties of the biotin repressor. A bifunctional
protein.";
J. Biol. Chem. 257:15167-15173(1982).
[9]
FUNCTION.
PubMed=2667763; DOI=10.1016/0092-8674(89)90421-2;
Cronan J.E. Jr.;
"The E. coli bio operon: transcriptional repression by an essential
protein modification enzyme.";
Cell 58:427-429(1989).
[10]
FUNCTION, AND CATALYTIC ACTIVITY.
PubMed=8003500; DOI=10.1021/bi00189a041;
Xu Y., Beckett D.;
"Kinetics of biotinyl-5'-adenylate synthesis catalyzed by the
Escherichia coli repressor of biotin biosynthesis and the stability of
the enzyme-product complex.";
Biochemistry 33:7354-7360(1994).
[11]
FUNCTION, DNA-BINDING, AND SUBUNIT.
PubMed=12527300; DOI=10.1016/S0022-2836(02)01308-6;
Streaker E.D., Beckett D.;
"Coupling of protein assembly and DNA binding: biotin repressor
dimerization precedes biotin operator binding.";
J. Mol. Biol. 325:937-948(2003).
[12]
DOMAIN, AND MUTAGENESIS OF THR-52; GLY-57 AND TYR-58.
STRAIN=K12;
PubMed=24189073; DOI=10.1074/jbc.M113.525618;
Chakravartty V., Cronan J.E.;
"The wing of a winged helix-turn-helix transcription factor organizes
the active site of BirA, a bifunctional repressor/ligase.";
J. Biol. Chem. 288:36029-36039(2013).
[13]
ENZYME REGULATION, SUBUNIT, AND INTERACTION WITH BCCP.
PubMed=23896299; DOI=10.1016/j.jmb.2013.07.029;
Adikaram P.R., Beckett D.;
"Protein:protein interactions in control of a transcriptional
switch.";
J. Mol. Biol. 425:4584-4594(2013).
[14]
X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) IN COMPLEX WITH BIOTIN, AND
DOMAIN.
PubMed=1409631; DOI=10.1073/pnas.89.19.9257;
Wilson K.P., Shewchuk L.M., Brennan R.G., Otsuka A.J., Matthews B.W.;
"Escherichia coli biotin holoenzyme synthetase/bio repressor crystal
structure delineates the biotin- and DNA-binding domains.";
Proc. Natl. Acad. Sci. U.S.A. 89:9257-9261(1992).
[15]
X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) IN COMPLEX WITH BIOTIN,
SUBUNIT, AND DOMAIN.
PubMed=11353844; DOI=10.1073/pnas.111128198;
Weaver L.H., Kwon K., Beckett D., Matthews B.W.;
"Corepressor-induced organization and assembly of the biotin
repressor: a model for allosteric activation of a transcriptional
regulator.";
Proc. Natl. Acad. Sci. U.S.A. 98:6045-6050(2001).
[16]
X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH
BIOTINOL-5'-AMP, SUBUNIT, AND DOMAIN.
PubMed=16438984; DOI=10.1016/j.jmb.2005.12.066;
Wood Z.A., Weaver L.H., Brown P.H., Beckett D., Matthews B.W.;
"Co-repressor induced order and biotin repressor dimerization: a case
for divergent followed by convergent evolution.";
J. Mol. Biol. 357:509-523(2006).
-!- FUNCTION: Acts both as a biotin--[acetyl-CoA-carboxylase] ligase
and a biotin-operon repressor. In the presence of ATP, BirA
activates biotin to form the BirA-biotinyl-5'-adenylate (BirA-bio-
5'-AMP or holoBirA) complex. HoloBirA can either transfer the
biotinyl moiety to the biotin carboxyl carrier protein (BCCP)
subunit of acetyl-CoA carboxylase, or bind to the biotin operator
site and inhibit transcription of the operon. {ECO:0000255|HAMAP-
Rule:MF_00978, ECO:0000269|PubMed:12527300,
ECO:0000269|PubMed:2667763, ECO:0000269|PubMed:6129246,
ECO:0000269|PubMed:8003500}.
-!- CATALYTIC ACTIVITY: ATP + biotin + apo-[acetyl-CoA:carbon-dioxide
ligase (ADP-forming)] = AMP + diphosphate + [acetyl-CoA:carbon-
dioxide ligase (ADP-forming)]. {ECO:0000255|HAMAP-Rule:MF_00978,
ECO:0000269|PubMed:6129246, ECO:0000269|PubMed:8003500}.
-!- ENZYME REGULATION: The switch between the enzymatic activity and
the repressor activity is regulated by cellular demand for biotin.
The switch occurs by swapping of protein interaction partners by
holoBirA. In conditions of high biotin demand, holoBirA associates
with apoBCCP to transfer biotin. In conditions of low biotin
demand, holoBirA dimerizes, binds DNA and represses transcription
of the biotin operon. {ECO:0000269|PubMed:23896299}.
-!- SUBUNIT: Monomer in solution. Interacts with BCCP. Homodimerizes
to bind DNA. Interaction with the corepressor bio-5'-AMP increases
dimerization. {ECO:0000269|PubMed:11353844,
ECO:0000269|PubMed:12527300, ECO:0000269|PubMed:1409631,
ECO:0000269|PubMed:16438984, ECO:0000269|PubMed:23896299,
ECO:0000269|PubMed:6129246}.
-!- DOMAIN: Contains an N-terminal helix-turn-helix DNA-binding
domain, connected via a linker to the central catalytic domain and
the C-terminal domain, which plays roles in dimerization,
catalytic function and DNA binding. The N-terminal domain is
required for both ligase and repressor activities. It may orient
the active site and thereby play an important role in enzymatic
activity. {ECO:0000269|PubMed:11353844,
ECO:0000269|PubMed:1409631, ECO:0000269|PubMed:16438984,
ECO:0000269|PubMed:24189073}.
-!- SIMILARITY: Belongs to the biotin--protein ligase family.
{ECO:0000255|HAMAP-Rule:MF_00978}.
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EMBL; M10123; AAA23520.1; -; Genomic_DNA.
EMBL; M15820; AAA23521.1; -; Genomic_DNA.
EMBL; L14557; AAA24186.1; -; Genomic_DNA.
EMBL; U00006; AAC43075.1; -; Genomic_DNA.
EMBL; U00096; AAC76951.1; -; Genomic_DNA.
EMBL; AP009048; BAE77342.1; -; Genomic_DNA.
PIR; B24029; BVECBF.
RefSeq; NP_418404.1; NC_000913.3.
RefSeq; WP_000654630.1; NZ_LN832404.1.
PDB; 1BIA; X-ray; 2.30 A; A=1-321.
PDB; 1BIB; X-ray; 2.80 A; A=1-321.
PDB; 1HXD; X-ray; 2.40 A; A/B=1-321.
PDB; 1K67; Model; -; A=65-317.
PDB; 2EWN; X-ray; 2.80 A; A/B=1-321.
PDB; 4WF2; X-ray; 2.31 A; A=1-321.
PDBsum; 1BIA; -.
PDBsum; 1BIB; -.
PDBsum; 1HXD; -.
PDBsum; 1K67; -.
PDBsum; 2EWN; -.
PDBsum; 4WF2; -.
DisProt; DP00349; -.
ProteinModelPortal; P06709; -.
SMR; P06709; -.
BioGrid; 4263391; 269.
DIP; DIP-9224N; -.
IntAct; P06709; 7.
MINT; MINT-1254106; -.
STRING; 316385.ECDH10B_4162; -.
BindingDB; P06709; -.
ChEMBL; CHEMBL3559644; -.
DrugBank; DB04651; BIOTINOL-5-AMP.
PaxDb; P06709; -.
PRIDE; P06709; -.
EnsemblBacteria; AAC76951; AAC76951; b3973.
EnsemblBacteria; BAE77342; BAE77342; BAE77342.
GeneID; 948469; -.
KEGG; ecj:JW3941; -.
KEGG; eco:b3973; -.
PATRIC; fig|1411691.4.peg.2735; -.
EchoBASE; EB0121; -.
EcoGene; EG10123; birA.
eggNOG; ENOG4105HJX; Bacteria.
eggNOG; COG0340; LUCA.
eggNOG; COG1654; LUCA.
HOGENOM; HOG000041812; -.
InParanoid; P06709; -.
KO; K03524; -.
PhylomeDB; P06709; -.
BioCyc; EcoCyc:BIOTINLIG-MONOMER; -.
BioCyc; MetaCyc:BIOTINLIG-MONOMER; -.
BRENDA; 6.3.4.15; 2026.
EvolutionaryTrace; P06709; -.
PRO; PR:P06709; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0017053; C:transcriptional repressor complex; IDA:CAFA.
GO; GO:0005524; F:ATP binding; IMP:CAFA.
GO; GO:0000984; F:bacterial-type RNA polymerase regulatory region sequence-specific DNA binding; IMP:CAFA.
GO; GO:0009374; F:biotin binding; IDA:CAFA.
GO; GO:0004077; F:biotin-[acetyl-CoA-carboxylase] ligase activity; IDA:EcoliWiki.
GO; GO:0003677; F:DNA binding; IDA:EcoliWiki.
GO; GO:0042803; F:protein homodimerization activity; IMP:CAFA.
GO; GO:0009102; P:biotin biosynthetic process; IMP:EcoliWiki.
GO; GO:0006768; P:biotin metabolic process; IMP:CAFA.
GO; GO:0009305; P:protein biotinylation; IDA:CACAO.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:UniProtKB-KW.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
CDD; cd16442; BPL; 1.
Gene3D; 1.10.10.10; -; 1.
HAMAP; MF_00978; Bifunct_BirA; 1.
InterPro; IPR030855; Bifunct_BirA.
InterPro; IPR004408; Biotin_CoA_COase_ligase.
InterPro; IPR004409; Biotin_operon_repress_HTH.
InterPro; IPR003142; BPL_C.
InterPro; IPR004143; BPL_LPL_catalytic.
InterPro; IPR013196; HTH_11.
InterPro; IPR008988; Transcriptional_repressor_C.
InterPro; IPR011991; WHTH_DNA-bd_dom.
PANTHER; PTHR12835:SF10; PTHR12835:SF10; 1.
Pfam; PF02237; BPL_C; 1.
Pfam; PF03099; BPL_LplA_LipB; 1.
Pfam; PF08279; HTH_11; 1.
SUPFAM; SSF46785; SSF46785; 1.
SUPFAM; SSF50037; SSF50037; 1.
TIGRFAMs; TIGR00121; birA_ligase; 1.
TIGRFAMs; TIGR00122; birA_repr_reg; 1.
PROSITE; PS51733; BPL_LPL_CATALYTIC; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Biotin; Complete proteome; DNA-binding;
Ligase; Nucleotide-binding; Reference proteome; Repressor;
Transcription; Transcription regulation.
CHAIN 1 321 Bifunctional ligase/repressor BirA.
/FTId=PRO_0000064932.
DOMAIN 67 254 BPL/LPL catalytic. {ECO:0000255|PROSITE-
ProRule:PRU01067}.
DNA_BIND 22 41 H-T-H motif. {ECO:0000255|HAMAP-
Rule:MF_00978}.
REGION 89 91 Biotin binding.
REGION 116 118 Biotin binding.
BINDING 112 112 Biotin. {ECO:0000255|HAMAP-Rule:MF_00978,
ECO:0000269|PubMed:11353844,
ECO:0000269|PubMed:1409631}.
BINDING 183 183 Biotin. {ECO:0000255|HAMAP-Rule:MF_00978,
ECO:0000269|PubMed:11353844,
ECO:0000269|PubMed:1409631}.
VARIANT 61 61 P -> A (in strain: RDD012).
VARIANT 70 70 K -> E (in strain: RDD012).
MUTAGEN 52 52 T->I: Does not affect repressor activity.
{ECO:0000269|PubMed:24189073}.
MUTAGEN 52 52 T->S: 5-fold increase of repressor
activity. Increases binding to DNA.
{ECO:0000269|PubMed:24189073}.
MUTAGEN 57 57 G->S: Lack of repressor activity. Does
not bind DNA.
{ECO:0000269|PubMed:24189073}.
MUTAGEN 58 58 Y->F: Lack of repressor activity.
{ECO:0000269|PubMed:24189073}.
MUTAGEN 58 58 Y->T: Does not affect repressor activity.
{ECO:0000269|PubMed:24189073}.
HELIX 5 14 {ECO:0000244|PDB:1BIA}.
HELIX 22 29 {ECO:0000244|PDB:1BIA}.
HELIX 33 45 {ECO:0000244|PDB:1BIA}.
STRAND 51 53 {ECO:0000244|PDB:1BIA}.
TURN 54 56 {ECO:0000244|PDB:1BIA}.
STRAND 57 59 {ECO:0000244|PDB:1BIA}.
HELIX 69 74 {ECO:0000244|PDB:1BIA}.
STRAND 76 79 {ECO:0000244|PDB:2EWN}.
STRAND 81 83 {ECO:0000244|PDB:1BIA}.
STRAND 85 88 {ECO:0000244|PDB:1BIA}.
HELIX 90 95 {ECO:0000244|PDB:1BIA}.
HELIX 96 100 {ECO:0000244|PDB:1BIA}.
STRAND 106 110 {ECO:0000244|PDB:1BIA}.
STRAND 129 139 {ECO:0000244|PDB:1BIA}.
HELIX 143 145 {ECO:0000244|PDB:2EWN}.
HELIX 147 163 {ECO:0000244|PDB:1BIA}.
STRAND 170 172 {ECO:0000244|PDB:1BIA}.
TURN 173 175 {ECO:0000244|PDB:1BIA}.
STRAND 176 179 {ECO:0000244|PDB:1BIA}.
STRAND 182 192 {ECO:0000244|PDB:1BIA}.
STRAND 195 197 {ECO:0000244|PDB:1HXD}.
STRAND 199 208 {ECO:0000244|PDB:1BIA}.
TURN 216 218 {ECO:0000244|PDB:2EWN}.
TURN 226 230 {ECO:0000244|PDB:1BIA}.
HELIX 235 256 {ECO:0000244|PDB:1BIA}.
HELIX 259 261 {ECO:0000244|PDB:1BIA}.
HELIX 262 268 {ECO:0000244|PDB:1BIA}.
TURN 270 273 {ECO:0000244|PDB:1BIA}.
STRAND 274 280 {ECO:0000244|PDB:1BIA}.
STRAND 283 292 {ECO:0000244|PDB:1BIA}.
TURN 294 296 {ECO:0000244|PDB:1HXD}.
STRAND 298 302 {ECO:0000244|PDB:1BIA}.
STRAND 305 311 {ECO:0000244|PDB:1BIA}.
STRAND 313 316 {ECO:0000244|PDB:1BIA}.
SEQUENCE 321 AA; 35312 MW; B80AEBCEEE1BD2D4 CRC64;
MKDNTVPLKL IALLANGEFH SGEQLGETLG MSRAAINKHI QTLRDWGVDV FTVPGKGYSL
PEPIQLLNAK QILGQLDGGS VAVLPVIDST NQYLLDRIGE LKSGDACIAE YQQAGRGRRG
RKWFSPFGAN LYLSMFWRLE QGPAAAIGLS LVIGIVMAEV LRKLGADKVR VKWPNDLYLQ
DRKLAGILVE LTGKTGDAAQ IVIGAGINMA MRRVEESVVN QGWITLQEAG INLDRNTLAA
MLIRELRAAL ELFEQEGLAP YLSRWEKLDN FINRPVKLII GDKEIFGISR GIDKQGALLL
EQDGIIKPWM GGEISLRSAE K


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