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Biotin synthase (EC 2.8.1.6)

 BIOB_ECOLI              Reviewed;         346 AA.
P12996; Q2MBJ4;
01-JAN-1990, integrated into UniProtKB/Swiss-Prot.
01-NOV-1997, sequence version 2.
05-JUL-2017, entry version 173.
RecName: Full=Biotin synthase;
EC=2.8.1.6 {ECO:0000269|PubMed:11862544, ECO:0000269|PubMed:17014080, ECO:0000269|PubMed:8142361};
Name=bioB; OrderedLocusNames=b0775, JW0758;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=3058702;
Otsuka A.J., Buoncristiani M.R., Howard P.K., Flamm J., Johnson O.,
Yamamoto R., Uchida K., Cook C., Ruppert J., Matsuzaki J.;
"The Escherichia coli biotin biosynthetic enzyme sequences predicted
from the nucleotide sequence of the bio operon.";
J. Biol. Chem. 263:19577-19585(1988).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Pearson B.M., McKee R.A.;
"Genetic material for expression of biotin synthetase enzymes.";
Patent number GB2216530, 11-OCT-1989.
[3]
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).
[4]
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).
[5]
PROTEIN SEQUENCE OF 1-17, FUNCTION, CATALYTIC ACTIVITY,
BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND SUBUNIT.
PubMed=8142361; DOI=10.1021/bi00178a020;
Sanyal I., Cohen G., Flint D.H.;
"Biotin synthase: purification, characterization as a [2Fe-2S] cluster
protein, and in vitro activity of the Escherichia coli bioB gene
product.";
Biochemistry 33:3625-3631(1994).
[6]
IDENTIFICATION BY 2D-GEL.
PubMed=9298644; DOI=10.1002/elps.1150180805;
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R.,
Neidhardt F.C.;
"Escherichia coli proteome analysis using the gene-protein database.";
Electrophoresis 18:1243-1251(1997).
[7]
MUTAGENESIS OF CYSTEINE RESIDUES.
PubMed=11686925; DOI=10.1093/oxfordjournals.jbchem.a003028;
Farh L., Hwang S.-Y., Steinrauf L., Chiang H.-J., Shiuan D.;
"Structure-function studies of Escherichia coli biotin synthase via a
chemical modification and site-directed mutagenesis approach.";
J. Biochem. 130:627-635(2001).
[8]
RESONANCE RAMAN SPECTROSCOPY, EPR SPECTROSCOPY, AND MOSSBAUER
SPECTROSCOPY.
PubMed=12440894; DOI=10.1021/ja0283044;
Cosper M.M., Jameson G.N.L., Davydov R., Eidsness M.K., Hoffman B.M.,
Huynh B.H., Johnson M.K.;
"The [4Fe-4S]2+ cluster in reconstituted biotin synthase binds S-
adenosyl-L-methionine.";
J. Am. Chem. Soc. 124:14006-14007(2002).
[9]
MUTAGENESIS OF CYS-53; CYS-57; CYS-60; CYS-97; CYS-128 AND CYS-188,
CATALYTIC ACTIVITY, EPR SPECTROSCOPY, AND MOSSBAUER SPECTROSCOPY.
PubMed=11834738; DOI=10.1074/jbc.M111324200;
Ollagnier-de Choudens S., Sanakis Y., Hewitson K.S., Roach P.,
Muenck E., Fontecave M.;
"Reductive cleavage of S-adenosylmethionine by biotin synthase from
Escherichia coli.";
J. Biol. Chem. 277:13449-13454(2002).
[10]
MUTAGENESIS OF CYS-53; CYS-57; CYS-60; CYS-97; CYS-128 AND CYS-188,
EPR SPECTROSCOPY, AND MOSSBAUER SPECTROSCOPY.
PubMed=11862544; DOI=10.1007/s007750100268;
Hewitson K.S., Ollagnier-de Choudens S., Sanakis Y., Shaw N.M.,
Baldwin J.E., Muenck E., Roach P.L., Fontecave M.;
"The iron-sulfur center of biotin synthase: site-directed mutants.";
J. Biol. Inorg. Chem. 7:83-93(2002).
[11]
ABSORPTION SPECTROSCOPY.
PubMed=12824504; DOI=10.1110/ps.0302203;
Cosper M.M., Cosper N.J., Hong W., Shokes J.E., Broderick W.E.,
Broderick J.B., Johnson M.K., Scott R.A.;
"Structural studies of the interaction of S-adenosylmethionine with
the [4Fe-4S] clusters in biotin synthase and pyruvate formate-lyase
activating enzyme.";
Protein Sci. 12:1573-1577(2003).
[12]
REACTION MECHANISM.
PubMed=19245793; DOI=10.1016/j.bbrc.2009.02.089;
Lotierzo M., Bui B.T., Leech H.K., Warren M.J., Marquet A.,
Rigby S.E.;
"Iron-sulfur cluster dynamics in biotin synthase: a new [2Fe-2S](1+)
cluster.";
Biochem. Biophys. Res. Commun. 381:487-490(2009).
[13]
MUTAGENESIS OF ASN-151; HIS-152; ASN-153 AND ASP-155, AND CATALYTIC
ACTIVITY.
PubMed=17014080; DOI=10.1021/bi060662m;
Lotierzo M., Raux E., Tse Sum Bui B., Goasdoue N., Libot F.,
Florentin D., Warren M.J., Marquet A.;
"Biotin synthase mechanism: mutagenesis of the YNHNLD conserved
motif.";
Biochemistry 45:12274-12281(2006).
[14]
X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS).
PubMed=14704425; DOI=10.1126/science.1088493;
Berkovitch F., Nicolet Y., Wan J.T., Jarrett J.T., Drennan C.L.;
"Crystal structure of biotin synthase, an S-adenosylmethionine-
dependent radical enzyme.";
Science 303:76-79(2004).
-!- FUNCTION: Catalyzes the conversion of dethiobiotin (DTB) to biotin
by the insertion of a sulfur atom into dethiobiotin via a radical-
based mechanism. {ECO:0000269|PubMed:8142361}.
-!- CATALYTIC ACTIVITY: Dethiobiotin + sulfur-(sulfur carrier) + 2 S-
adenosyl-L-methionine + 2 reduced [2Fe-2S] ferredoxin = biotin +
(sulfur carrier) + 2 L-methionine + 2 5'-deoxyadenosine + 2
oxidized [2Fe-2S] ferredoxin. {ECO:0000269|PubMed:11862544,
ECO:0000269|PubMed:17014080, ECO:0000269|PubMed:8142361}.
-!- COFACTOR:
Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
Evidence={ECO:0000269|PubMed:8142361};
Note=Binds 1 [4Fe-4S] cluster. The cluster is coordinated with 3
cysteines and an exchangeable S-adenosyl-L-methionine.
{ECO:0000269|PubMed:8142361};
-!- COFACTOR:
Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:49601;
Evidence={ECO:0000269|PubMed:8142361};
Note=Binds 1 [2Fe-2S] cluster. The cluster is coordinated with 3
cysteines and 1 arginine. {ECO:0000269|PubMed:8142361};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=2 uM for dethiobiotin {ECO:0000269|PubMed:8142361};
-!- PATHWAY: Cofactor biosynthesis; biotin biosynthesis; biotin from
7,8-diaminononanoate: step 2/2.
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:8142361}.
-!- INTERACTION:
Q47147:yafJ; NbExp=4; IntAct=EBI-557917, EBI-1114805;
-!- SIMILARITY: Belongs to the radical SAM superfamily. Biotin
synthase family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; J04423; AAA23515.1; -; Genomic_DNA.
EMBL; A11530; CAA00965.1; -; Unassigned_DNA.
EMBL; U00096; AAC73862.1; -; Genomic_DNA.
EMBL; AP009048; BAE76362.1; -; Genomic_DNA.
PIR; JC2517; SYECBB.
RefSeq; NP_415296.1; NC_000913.3.
RefSeq; WP_000951213.1; NZ_LN832404.1.
PDB; 1R30; X-ray; 3.40 A; A/B=2-346.
PDBsum; 1R30; -.
ProteinModelPortal; P12996; -.
SMR; P12996; -.
BioGrid; 4259949; 7.
DIP; DIP-9220N; -.
IntAct; P12996; 17.
MINT; MINT-1292998; -.
STRING; 316385.ECDH10B_0843; -.
DrugBank; DB03775; D-Dethiobiotin.
DrugBank; DB03754; Tris.
PaxDb; P12996; -.
PRIDE; P12996; -.
EnsemblBacteria; AAC73862; AAC73862; b0775.
EnsemblBacteria; BAE76362; BAE76362; BAE76362.
GeneID; 945370; -.
KEGG; ecj:JW0758; -.
KEGG; eco:b0775; -.
PATRIC; fig|1411691.4.peg.1503; -.
EchoBASE; EB0116; -.
EcoGene; EG10118; bioB.
eggNOG; ENOG4105CZF; Bacteria.
eggNOG; COG0502; LUCA.
HOGENOM; HOG000239957; -.
InParanoid; P12996; -.
KO; K01012; -.
PhylomeDB; P12996; -.
BioCyc; EcoCyc:BIOTIN-SYN-MONOMER; -.
BioCyc; MetaCyc:BIOTIN-SYN-MONOMER; -.
BRENDA; 2.8.1.6; 2026.
SABIO-RK; P12996; -.
UniPathway; UPA00078; UER00162.
EvolutionaryTrace; P12996; -.
PRO; PR:P12996; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IDA:EcoCyc.
GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:EcoCyc.
GO; GO:0004076; F:biotin synthase activity; IDA:EcoCyc.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0009102; P:biotin biosynthetic process; IMP:EcoCyc.
Gene3D; 3.20.20.70; -; 1.
HAMAP; MF_01694; BioB; 1.
InterPro; IPR013785; Aldolase_TIM.
InterPro; IPR010722; BATS_dom.
InterPro; IPR002684; Biotin_synth/BioAB.
InterPro; IPR024177; Biotin_synthase.
InterPro; IPR006638; Elp3/MiaB/NifB.
InterPro; IPR007197; rSAM.
PANTHER; PTHR22976; PTHR22976; 1.
PANTHER; PTHR22976:SF32; PTHR22976:SF32; 1.
Pfam; PF06968; BATS; 1.
Pfam; PF04055; Radical_SAM; 1.
PIRSF; PIRSF001619; Biotin_synth; 1.
SFLD; SFLDF00272; biotin_synthase; 1.
SFLD; SFLDG01278; biotin_synthase_like; 1.
SFLD; SFLDS00029; Radical_SAM; 1.
SMART; SM00876; BATS; 1.
SMART; SM00729; Elp3; 1.
TIGRFAMs; TIGR00433; bioB; 1.
1: Evidence at protein level;
2Fe-2S; 3D-structure; 4Fe-4S; Biotin biosynthesis; Complete proteome;
Direct protein sequencing; Iron; Iron-sulfur; Metal-binding;
Reference proteome; S-adenosyl-L-methionine; Transferase.
CHAIN 1 346 Biotin synthase.
/FTId=PRO_0000185552.
METAL 53 53 Iron-sulfur 1 (4Fe-4S-S-AdoMet).
METAL 57 57 Iron-sulfur 1 (4Fe-4S-S-AdoMet).
METAL 60 60 Iron-sulfur 1 (4Fe-4S-S-AdoMet).
METAL 97 97 Iron-sulfur 2 (2Fe-2S).
METAL 128 128 Iron-sulfur 2 (2Fe-2S).
METAL 188 188 Iron-sulfur 2 (2Fe-2S).
METAL 260 260 Iron-sulfur 2 (2Fe-2S).
MUTAGEN 53 53 C->A: Total loss of activity.
{ECO:0000269|PubMed:11834738,
ECO:0000269|PubMed:11862544}.
MUTAGEN 57 57 C->A: Total loss of activity.
{ECO:0000269|PubMed:11834738,
ECO:0000269|PubMed:11862544}.
MUTAGEN 60 60 C->A: Total loss of activity.
{ECO:0000269|PubMed:11834738,
ECO:0000269|PubMed:11862544}.
MUTAGEN 97 97 C->A: Total loss of activity.
{ECO:0000269|PubMed:11834738,
ECO:0000269|PubMed:11862544}.
MUTAGEN 128 128 C->A: Total loss of activity.
{ECO:0000269|PubMed:11834738,
ECO:0000269|PubMed:11862544}.
MUTAGEN 151 151 N->A: Total loss of activity.
{ECO:0000269|PubMed:17014080}.
MUTAGEN 152 152 H->A: Weak activity.
{ECO:0000269|PubMed:17014080}.
MUTAGEN 153 153 N->A: Total loss of activity.
{ECO:0000269|PubMed:17014080}.
MUTAGEN 155 155 D->A: Total loss of activity.
{ECO:0000269|PubMed:17014080}.
MUTAGEN 188 188 C->A: Total loss of activity.
{ECO:0000269|PubMed:11834738,
ECO:0000269|PubMed:11862544}.
CONFLICT 63 63 S -> T (in Ref. 1; AAA23515).
{ECO:0000305}.
TURN 10 12 {ECO:0000244|PDB:1R30}.
HELIX 13 17 {ECO:0000244|PDB:1R30}.
HELIX 20 34 {ECO:0000244|PDB:1R30}.
STRAND 41 49 {ECO:0000244|PDB:1R30}.
STRAND 53 55 {ECO:0000244|PDB:1R30}.
HELIX 78 90 {ECO:0000244|PDB:1R30}.
STRAND 94 100 {ECO:0000244|PDB:1R30}.
TURN 107 109 {ECO:0000244|PDB:1R30}.
HELIX 110 122 {ECO:0000244|PDB:1R30}.
STRAND 125 130 {ECO:0000244|PDB:1R30}.
HELIX 136 145 {ECO:0000244|PDB:1R30}.
STRAND 149 151 {ECO:0000244|PDB:1R30}.
HELIX 158 164 {ECO:0000244|PDB:1R30}.
HELIX 170 184 {ECO:0000244|PDB:1R30}.
STRAND 186 188 {ECO:0000244|PDB:1R30}.
STRAND 191 193 {ECO:0000244|PDB:1R30}.
HELIX 199 210 {ECO:0000244|PDB:1R30}.
STRAND 211 214 {ECO:0000244|PDB:1R30}.
STRAND 217 223 {ECO:0000244|PDB:1R30}.
HELIX 240 253 {ECO:0000244|PDB:1R30}.
STRAND 257 264 {ECO:0000244|PDB:1R30}.
HELIX 265 267 {ECO:0000244|PDB:1R30}.
HELIX 270 279 {ECO:0000244|PDB:1R30}.
STRAND 283 285 {ECO:0000244|PDB:1R30}.
STRAND 287 294 {ECO:0000244|PDB:1R30}.
HELIX 298 307 {ECO:0000244|PDB:1R30}.
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


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