BIOB_ECOLI
ID BIOB_ECOLI Reviewed; 346 AA.
AC P12996; Q2MBJ4;
DT 01-JAN-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 200.
DE RecName: Full=Biotin synthase;
DE EC=2.8.1.6 {ECO:0000269|PubMed:11862544, ECO:0000269|PubMed:17014080, ECO:0000269|PubMed:8142361};
GN Name=bioB; OrderedLocusNames=b0775, JW0758;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=3058702; DOI=10.1016/s0021-9258(19)77675-3;
RA Otsuka A.J., Buoncristiani M.R., Howard P.K., Flamm J., Johnson O.,
RA Yamamoto R., Uchida K., Cook C., Ruppert J., Matsuzaki J.;
RT "The Escherichia coli biotin biosynthetic enzyme sequences predicted from
RT the nucleotide sequence of the bio operon.";
RL J. Biol. Chem. 263:19577-19585(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Pearson B.M., McKee R.A.;
RT "Genetic material for expression of biotin synthetase enzymes.";
RL Patent number GB2216530, 11-OCT-1989.
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 1-17, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, COFACTOR, AND SUBUNIT.
RX PubMed=8142361; DOI=10.1021/bi00178a020;
RA Sanyal I., Cohen G., Flint D.H.;
RT "Biotin synthase: purification, characterization as a [2Fe-2S] cluster
RT protein, and in vitro activity of the Escherichia coli bioB gene product.";
RL Biochemistry 33:3625-3631(1994).
RN [6]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [7]
RP MUTAGENESIS OF CYSTEINE RESIDUES.
RX PubMed=11686925; DOI=10.1093/oxfordjournals.jbchem.a003028;
RA Farh L., Hwang S.-Y., Steinrauf L., Chiang H.-J., Shiuan D.;
RT "Structure-function studies of Escherichia coli biotin synthase via a
RT chemical modification and site-directed mutagenesis approach.";
RL J. Biochem. 130:627-635(2001).
RN [8]
RP RESONANCE RAMAN SPECTROSCOPY, EPR SPECTROSCOPY, AND MOSSBAUER SPECTROSCOPY.
RX PubMed=12440894; DOI=10.1021/ja0283044;
RA Cosper M.M., Jameson G.N.L., Davydov R., Eidsness M.K., Hoffman B.M.,
RA Huynh B.H., Johnson M.K.;
RT "The [4Fe-4S]2+ cluster in reconstituted biotin synthase binds S-adenosyl-
RT L-methionine.";
RL J. Am. Chem. Soc. 124:14006-14007(2002).
RN [9]
RP MUTAGENESIS OF CYS-53; CYS-57; CYS-60; CYS-97; CYS-128 AND CYS-188,
RP CATALYTIC ACTIVITY, EPR SPECTROSCOPY, AND MOSSBAUER SPECTROSCOPY.
RX PubMed=11834738; DOI=10.1074/jbc.m111324200;
RA Ollagnier-de Choudens S., Sanakis Y., Hewitson K.S., Roach P., Muenck E.,
RA Fontecave M.;
RT "Reductive cleavage of S-adenosylmethionine by biotin synthase from
RT Escherichia coli.";
RL J. Biol. Chem. 277:13449-13454(2002).
RN [10]
RP MUTAGENESIS OF CYS-53; CYS-57; CYS-60; CYS-97; CYS-128 AND CYS-188, EPR
RP SPECTROSCOPY, AND MOSSBAUER SPECTROSCOPY.
RX PubMed=11862544; DOI=10.1007/s007750100268;
RA Hewitson K.S., Ollagnier-de Choudens S., Sanakis Y., Shaw N.M.,
RA Baldwin J.E., Muenck E., Roach P.L., Fontecave M.;
RT "The iron-sulfur center of biotin synthase: site-directed mutants.";
RL J. Biol. Inorg. Chem. 7:83-93(2002).
RN [11]
RP ABSORPTION SPECTROSCOPY.
RX PubMed=12824504; DOI=10.1110/ps.0302203;
RA Cosper M.M., Cosper N.J., Hong W., Shokes J.E., Broderick W.E.,
RA Broderick J.B., Johnson M.K., Scott R.A.;
RT "Structural studies of the interaction of S-adenosylmethionine with the
RT [4Fe-4S] clusters in biotin synthase and pyruvate formate-lyase activating
RT enzyme.";
RL Protein Sci. 12:1573-1577(2003).
RN [12]
RP ACTIVITY REGULATION.
RX PubMed=15911379; DOI=10.1016/j.chembiol.2005.04.012;
RA Choi-Rhee E., Cronan J.E.;
RT "A nucleosidase required for in vivo function of the S-adenosyl-L-
RT methionine radical enzyme, biotin synthase.";
RL Chem. Biol. 12:589-593(2005).
RN [13]
RP REACTION MECHANISM.
RX PubMed=19245793; DOI=10.1016/j.bbrc.2009.02.089;
RA Lotierzo M., Bui B.T., Leech H.K., Warren M.J., Marquet A., Rigby S.E.;
RT "Iron-sulfur cluster dynamics in biotin synthase: a new [2Fe-2S](1+)
RT cluster.";
RL Biochem. Biophys. Res. Commun. 381:487-490(2009).
RN [14]
RP MUTAGENESIS OF ASN-151; HIS-152; ASN-153 AND ASP-155, AND CATALYTIC
RP ACTIVITY.
RX PubMed=17014080; DOI=10.1021/bi060662m;
RA Lotierzo M., Raux E., Tse Sum Bui B., Goasdoue N., Libot F., Florentin D.,
RA Warren M.J., Marquet A.;
RT "Biotin synthase mechanism: mutagenesis of the YNHNLD conserved motif.";
RL Biochemistry 45:12274-12281(2006).
RN [15]
RP X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS).
RX PubMed=14704425; DOI=10.1126/science.1088493;
RA Berkovitch F., Nicolet Y., Wan J.T., Jarrett J.T., Drennan C.L.;
RT "Crystal structure of biotin synthase, an S-adenosylmethionine-dependent
RT radical enzyme.";
RL Science 303:76-79(2004).
CC -!- FUNCTION: Catalyzes the conversion of dethiobiotin (DTB) to biotin by
CC the insertion of a sulfur atom into dethiobiotin via a radical-based
CC mechanism. {ECO:0000269|PubMed:8142361}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-
CC 2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2 5'-deoxyadenosine +
CC [sulfur carrier]-H + biotin + 2 L-methionine + 2 oxidized [2Fe-2S]-
CC [ferredoxin]; Xref=Rhea:RHEA:22060, Rhea:RHEA-COMP:10000, Rhea:RHEA-
CC COMP:10001, Rhea:RHEA-COMP:14737, Rhea:RHEA-COMP:14739,
CC ChEBI:CHEBI:17319, ChEBI:CHEBI:29917, ChEBI:CHEBI:33737,
CC ChEBI:CHEBI:33738, ChEBI:CHEBI:57586, ChEBI:CHEBI:57844,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:64428, ChEBI:CHEBI:149473; EC=2.8.1.6;
CC Evidence={ECO:0000269|PubMed:11862544, ECO:0000269|PubMed:17014080,
CC ECO:0000269|PubMed:8142361};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:8142361};
CC Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000269|PubMed:8142361};
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Evidence={ECO:0000269|PubMed:8142361};
CC Note=Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3
CC cysteines and 1 arginine. {ECO:0000269|PubMed:8142361};
CC -!- ACTIVITY REGULATION: Is physiologically inhibited by accumulation of
CC the reaction product 5'-deoxyadenosine. {ECO:0000269|PubMed:15911379}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2 uM for dethiobiotin {ECO:0000269|PubMed:8142361};
CC -!- PATHWAY: Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-
CC diaminononanoate: step 2/2.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:8142361}.
CC -!- INTERACTION:
CC P12996; Q47147: yafJ; NbExp=4; IntAct=EBI-557917, EBI-1114805;
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. Biotin synthase
CC family. {ECO:0000305}.
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DR EMBL; J04423; AAA23515.1; -; Genomic_DNA.
DR EMBL; A11530; CAA00965.1; -; Unassigned_DNA.
DR EMBL; U00096; AAC73862.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76362.1; -; Genomic_DNA.
DR PIR; JC2517; SYECBB.
DR RefSeq; NP_415296.1; NC_000913.3.
DR RefSeq; WP_000951213.1; NZ_SSZK01000002.1.
DR PDB; 1R30; X-ray; 3.40 A; A/B=2-346.
DR PDBsum; 1R30; -.
DR AlphaFoldDB; P12996; -.
DR SMR; P12996; -.
DR BioGRID; 4259949; 37.
DR BioGRID; 849746; 13.
DR DIP; DIP-9220N; -.
DR IntAct; P12996; 17.
DR STRING; 511145.b0775; -.
DR DrugBank; DB03775; Dethiobiotin.
DR PaxDb; P12996; -.
DR PRIDE; P12996; -.
DR EnsemblBacteria; AAC73862; AAC73862; b0775.
DR EnsemblBacteria; BAE76362; BAE76362; BAE76362.
DR GeneID; 67413814; -.
DR GeneID; 945370; -.
DR KEGG; ecj:JW0758; -.
DR KEGG; eco:b0775; -.
DR PATRIC; fig|1411691.4.peg.1503; -.
DR EchoBASE; EB0116; -.
DR eggNOG; COG0502; Bacteria.
DR HOGENOM; CLU_033172_1_2_6; -.
DR InParanoid; P12996; -.
DR OMA; ADRFCMG; -.
DR PhylomeDB; P12996; -.
DR BioCyc; EcoCyc:BIOTIN-SYN-MON; -.
DR BioCyc; MetaCyc:BIOTIN-SYN-MON; -.
DR BRENDA; 2.8.1.6; 2026.
DR SABIO-RK; P12996; -.
DR UniPathway; UPA00078; UER00162.
DR EvolutionaryTrace; P12996; -.
DR PRO; PR:P12996; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IDA:EcoCyc.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:EcoCyc.
DR GO; GO:0004076; F:biotin synthase activity; IDA:EcoCyc.
DR GO; GO:0005506; F:iron ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009102; P:biotin biosynthetic process; IMP:EcoCyc.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_01694; BioB; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR010722; BATS_dom.
DR InterPro; IPR002684; Biotin_synth/BioAB.
DR InterPro; IPR024177; Biotin_synthase.
DR InterPro; IPR006638; Elp3/MiaB/NifB.
DR InterPro; IPR007197; rSAM.
DR PANTHER; PTHR22976; PTHR22976; 1.
DR Pfam; PF06968; BATS; 1.
DR Pfam; PF04055; Radical_SAM; 1.
DR PIRSF; PIRSF001619; Biotin_synth; 1.
DR SFLD; SFLDF00272; biotin_synthase; 1.
DR SMART; SM00876; BATS; 1.
DR SMART; SM00729; Elp3; 1.
DR TIGRFAMs; TIGR00433; bioB; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 2Fe-2S; 3D-structure; 4Fe-4S; Biotin biosynthesis;
KW Direct protein sequencing; Iron; Iron-sulfur; Metal-binding;
KW Reference proteome; S-adenosyl-L-methionine; Transferase.
FT CHAIN 1..346
FT /note="Biotin synthase"
FT /id="PRO_0000185552"
FT DOMAIN 38..256
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 53
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT BINDING 57
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT BINDING 60
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT BINDING 97
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT BINDING 128
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT BINDING 188
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT BINDING 260
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT MUTAGEN 53
FT /note="C->A: Total loss of activity."
FT /evidence="ECO:0000269|PubMed:11834738,
FT ECO:0000269|PubMed:11862544"
FT MUTAGEN 57
FT /note="C->A: Total loss of activity."
FT /evidence="ECO:0000269|PubMed:11834738,
FT ECO:0000269|PubMed:11862544"
FT MUTAGEN 60
FT /note="C->A: Total loss of activity."
FT /evidence="ECO:0000269|PubMed:11834738,
FT ECO:0000269|PubMed:11862544"
FT MUTAGEN 97
FT /note="C->A: Total loss of activity."
FT /evidence="ECO:0000269|PubMed:11834738,
FT ECO:0000269|PubMed:11862544"
FT MUTAGEN 128
FT /note="C->A: Total loss of activity."
FT /evidence="ECO:0000269|PubMed:11834738,
FT ECO:0000269|PubMed:11862544"
FT MUTAGEN 151
FT /note="N->A: Total loss of activity."
FT /evidence="ECO:0000269|PubMed:17014080"
FT MUTAGEN 152
FT /note="H->A: Weak activity."
FT /evidence="ECO:0000269|PubMed:17014080"
FT MUTAGEN 153
FT /note="N->A: Total loss of activity."
FT /evidence="ECO:0000269|PubMed:17014080"
FT MUTAGEN 155
FT /note="D->A: Total loss of activity."
FT /evidence="ECO:0000269|PubMed:17014080"
FT MUTAGEN 188
FT /note="C->A: Total loss of activity."
FT /evidence="ECO:0000269|PubMed:11834738,
FT ECO:0000269|PubMed:11862544"
FT CONFLICT 63
FT /note="S -> T (in Ref. 1; AAA23515)"
FT /evidence="ECO:0000305"
FT TURN 10..12
FT /evidence="ECO:0007829|PDB:1R30"
FT HELIX 13..17
FT /evidence="ECO:0007829|PDB:1R30"
FT HELIX 20..34
FT /evidence="ECO:0007829|PDB:1R30"
FT STRAND 41..49
FT /evidence="ECO:0007829|PDB:1R30"
FT STRAND 53..55
FT /evidence="ECO:0007829|PDB:1R30"
FT HELIX 78..90
FT /evidence="ECO:0007829|PDB:1R30"
FT STRAND 94..100
FT /evidence="ECO:0007829|PDB:1R30"
FT TURN 107..109
FT /evidence="ECO:0007829|PDB:1R30"
FT HELIX 110..122
FT /evidence="ECO:0007829|PDB:1R30"
FT STRAND 125..130
FT /evidence="ECO:0007829|PDB:1R30"
FT HELIX 136..145
FT /evidence="ECO:0007829|PDB:1R30"
FT STRAND 149..151
FT /evidence="ECO:0007829|PDB:1R30"
FT HELIX 158..164
FT /evidence="ECO:0007829|PDB:1R30"
FT HELIX 170..184
FT /evidence="ECO:0007829|PDB:1R30"
FT STRAND 186..188
FT /evidence="ECO:0007829|PDB:1R30"
FT STRAND 191..193
FT /evidence="ECO:0007829|PDB:1R30"
FT HELIX 199..210
FT /evidence="ECO:0007829|PDB:1R30"
FT STRAND 211..214
FT /evidence="ECO:0007829|PDB:1R30"
FT STRAND 217..223
FT /evidence="ECO:0007829|PDB:1R30"
FT HELIX 240..253
FT /evidence="ECO:0007829|PDB:1R30"
FT STRAND 257..264
FT /evidence="ECO:0007829|PDB:1R30"
FT HELIX 265..267
FT /evidence="ECO:0007829|PDB:1R30"
FT HELIX 270..279
FT /evidence="ECO:0007829|PDB:1R30"
FT STRAND 283..285
FT /evidence="ECO:0007829|PDB:1R30"
FT STRAND 287..294
FT /evidence="ECO:0007829|PDB:1R30"
FT HELIX 298..307
FT /evidence="ECO:0007829|PDB:1R30"
SQ SEQUENCE 346 AA; 38648 MW; 550A7899A2DF6082 CRC64;
MAHRPRWTLS QVTELFEKPL LDLLFEAQQV HRQHFDPRQV QVSTLLSIKT GACPEDCKYC
PQSSRYKTGL EAERLMEVEQ VLESARKAKA AGSTRFCMGA AWKNPHERDM PYLEQMVQGV
KAMGLEACMT LGTLSESQAQ RLANAGLDYY NHNLDTSPEF YGNIITTRTY QERLDTLEKV
RDAGIKVCSG GIVGLGETVK DRAGLLLQLA NLPTPPESVP INMLVKVKGT PLADNDDVDA
FDFIRTIAVA RIMMPTSYVR LSAGREQMNE QTQAMCFMAG ANSIFYGCKL LTTPNPEEDK
DLQLFRKLGL NPQQTAVLAG DNEQQQRLEQ ALMTPDTDEY YNAAAL
