P12996 (BIOB_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Biotin synthase
EC=2.8.1.6

Gene names

Name:	bioB
Ordered Locus Names:	b0775, JW0758

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia › Escherichia coli

Protein attributes

Sequence length	346 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical-based mechanism. Ref.5
Catalytic activity	Dethiobiotin + sulfur + 2 S-adenosyl-L-methionine = biotin + 2 L-methionine + 2 5'-deoxyadenosine. HAMAP-Rule MF_01694
Cofactor	Binds 1 4Fe-4S cluster. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Ref.5 Binds 1 2Fe-2S cluster. The cluster is coordinated with 3 cysteines and 1 arginine. Ref.5
Pathway	Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 2/2. HAMAP-Rule MF_01694
Subunit structure	Homodimer. Ref.5
Sequence similarities	Belongs to the radical SAM superfamily. Biotin synthase family.
Biophysicochemical properties	Kinetic parameters: KM=2 µM for dethiobiotin Ref.5

Ontologies

Keywords
Biological process	Biotin biosynthesis
Ligand	2Fe-2S 4Fe-4S Iron Iron-sulfur Metal-binding S-adenosyl-L-methionine
Molecular function	Transferase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	biotin biosynthetic process Inferred from mutant phenotype PubMed 4921685. Source: EcoCyc
Molecular_function	2 iron, 2 sulfur cluster binding Inferred from direct assay PubMed 14967041. Source: EcoCyc 4 iron, 4 sulfur cluster binding Inferred from direct assay PubMed 14967041. Source: EcoCyc biotin synthase activity Inferred from direct assay Ref.13. Source: EcoCyc iron ion binding Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 346

346

Biotin synthase HAMAP-Rule MF_01694

PRO_0000185552

Sites

Metal binding

53

1

Iron-sulfur 1 (4Fe-4S-S-AdoMet)

Metal binding

57

1

Iron-sulfur 1 (4Fe-4S-S-AdoMet)

Metal binding

60

1

Iron-sulfur 1 (4Fe-4S-S-AdoMet)

Metal binding

97

1

Iron-sulfur 2 (2Fe-2S)

Metal binding

128

1

Iron-sulfur 2 (2Fe-2S)

Metal binding

188

1

Iron-sulfur 2 (2Fe-2S)

Metal binding

260

1

Iron-sulfur 2 (2Fe-2S)

Experimental info

Mutagenesis

53

1

C → A: Total loss of activity. Ref.7 Ref.9 Ref.10

Mutagenesis

57

1

C → A: Total loss of activity. Ref.7 Ref.9 Ref.10

Mutagenesis

60

1

C → A: Total loss of activity. Ref.7 Ref.9 Ref.10

Mutagenesis

97

1

C → A: Total loss of activity. Ref.7 Ref.9 Ref.10

Mutagenesis

128

1

C → A: Total loss of activity. Ref.7 Ref.9 Ref.10

Mutagenesis

151

1

N → A: Total loss of activity. Ref.7 Ref.13

Mutagenesis

152

1

H → A: Weak activity. Ref.7 Ref.13

Mutagenesis

153

1

N → A: Total loss of activity. Ref.7 Ref.13

Mutagenesis

155

1

D → A: Total loss of activity. Ref.7 Ref.13

Mutagenesis

188

1

C → A: Total loss of activity. Ref.7 Ref.9 Ref.10

Sequence conflict

63

1

S → T in AAA23515. Ref.1

Secondary structure

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346

Helix Strand Turn

Details...

Turn

10 – 12

3

Helix

13 – 17

5

Helix

20 – 34

15

Beta strand

41 – 49

9

Beta strand

53 – 55

3

Helix

78 – 90

13

Beta strand

94 – 100

7

Turn

107 – 109

3

Helix

110 – 122

13

Beta strand

125 – 130

6

Helix

136 – 145

10

Beta strand

149 – 151

3

Helix

158 – 164

7

Helix

170 – 184

15

Beta strand

186 – 188

3

Beta strand

191 – 193

3

Helix

199 – 210

12

Beta strand

211 – 214

4

Beta strand

217 – 223

7

Helix

240 – 253

14

Beta strand

257 – 264

8

Helix

265 – 267

3

Helix

270 – 279

10

Beta strand

283 – 285

3

Beta strand

287 – 294

8

Helix

298 – 307

10

Sequences

	Sequence		Length	Mass (Da)
	P12996 [UniParc]. Last modified November 1, 1997. Version 2. Checksum: 550A7899A2DF6082	FASTA	346	38,648
	10 20 30 40 50 60 MAHRPRWTLS QVTELFEKPL LDLLFEAQQV HRQHFDPRQV QVSTLLSIKT GACPEDCKYC 70 80 90 100 110 120 PQSSRYKTGL EAERLMEVEQ VLESARKAKA AGSTRFCMGA AWKNPHERDM PYLEQMVQGV 130 140 150 160 170 180 KAMGLEACMT LGTLSESQAQ RLANAGLDYY NHNLDTSPEF YGNIITTRTY QERLDTLEKV 190 200 210 220 230 240 RDAGIKVCSG GIVGLGETVK DRAGLLLQLA NLPTPPESVP INMLVKVKGT PLADNDDVDA 250 260 270 280 290 300 FDFIRTIAVA RIMMPTSYVR LSAGREQMNE QTQAMCFMAG ANSIFYGCKL LTTPNPEEDK 310 320 330 340 DLQLFRKLGL NPQQTAVLAG DNEQQQRLEQ ALMTPDTDEY YNAAAL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon." Otsuka A.J., Buoncristiani M.R., Howard P.K., Flamm J., Johnson O., Yamamoto R., Uchida K., Cook C., Ruppert J., Matsuzaki J. J. Biol. Chem. 263:19577-19585(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Genetic material for expression of biotin synthetase enzymes." Pearson B.M., McKee R.A. Patent number GB2216530, 11-OCT-1989 Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"The complete genome sequence of Escherichia coli K-12." 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. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Biotin synthase: purification, characterization as a [2Fe-2S] cluster protein, and in vitro activity of the Escherichia coli bioB gene product." Sanyal I., Cohen G., Flint D.H. Biochemistry 33:3625-3631(1994) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 1-17, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, SUBUNIT.
[6]	"Escherichia coli proteome analysis using the gene-protein database." VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C. Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY 2D-GEL.
[7]	"Structure-function studies of Escherichia coli biotin synthase via a chemical modification and site-directed mutagenesis approach." Farh L., Hwang S.-Y., Steinrauf L., Chiang H.-J., Shiuan D. J. Biochem. 130:627-635(2001) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF CYSTEINE RESIDUES.
[8]	"The [4Fe-4S]2+ cluster in reconstituted biotin synthase binds S-adenosyl-L-methionine." Cosper M.M., Jameson G.N.L., Davydov R., Eidsness M.K., Hoffman B.M., Huynh B.H., Johnson M.K. J. Am. Chem. Soc. 124:14006-14007(2002) [PubMed] [Europe PMC] [Abstract] Cited for: RESONANCE RAMAN SPECTROSCOPY, EPR SPECTROSCOPY, MOSSBAUER SPECTROSCOPY.
[9]	"Reductive cleavage of S-adenosylmethionine by biotin synthase from Escherichia coli." Ollagnier-de Choudens S., Sanakis Y., Hewitson K.S., Roach P., Muenck E., Fontecave M. J. Biol. Chem. 277:13449-13454(2002) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF CYS-53; CYS-57; CYS-60; CYS-97; CYS-128 AND CYS-188, EPR SPECTROSCOPY, MOSSBAUER SPECTROSCOPY.
[10]	"The iron-sulfur center of biotin synthase: site-directed mutants." Hewitson K.S., Ollagnier-de Choudens S., Sanakis Y., Shaw N.M., Baldwin J.E., Muenck E., Roach P.L., Fontecave M. J. Biol. Inorg. Chem. 7:83-93(2002) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF CYS-53; CYS-57; CYS-60; CYS-97; CYS-128 AND CYS-188, EPR SPECTROSCOPY, MOSSBAUER SPECTROSCOPY.
[11]	"Structural studies of the interaction of S-adenosylmethionine with the [4Fe-4S] clusters in biotin synthase and pyruvate formate-lyase activating enzyme." Cosper M.M., Cosper N.J., Hong W., Shokes J.E., Broderick W.E., Broderick J.B., Johnson M.K., Scott R.A. Protein Sci. 12:1573-1577(2003) [PubMed] [Europe PMC] [Abstract] Cited for: ABSORPTION SPECTROSCOPY.
[12]	"Iron-sulfur cluster dynamics in biotin synthase: a new [2Fe-2S](1+) cluster." Lotierzo M., Bui B.T., Leech H.K., Warren M.J., Marquet A., Rigby S.E. Biochem. Biophys. Res. Commun. 381:487-490(2009) [PubMed] [Europe PMC] [Abstract] Cited for: REACTION MECHANISM.
[13]	"Biotin synthase mechanism: mutagenesis of the YNHNLD conserved motif." Lotierzo M., Raux E., Tse Sum Bui B., Goasdoue N., Libot F., Florentin D., Warren M.J., Marquet A. Biochemistry 45:12274-12281(2006) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ASN-151; HIS-152; ASN-153 AND ASP-155.
[14]	"Crystal structure of biotin synthase, an S-adenosylmethionine-dependent radical enzyme." Berkovitch F., Nicolet Y., Wan J.T., Jarrett J.T., Drennan C.L. Science 303:76-79(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.4 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

J04423 Genomic DNA. Translation: AAA23515.1.
A11530 Unassigned DNA. Translation: CAA00965.1.
U00096 Genomic DNA. Translation: AAC73862.1.
AP009048 Genomic DNA. Translation: BAE76362.1.

PIR

SYECBB. JC2517.

RefSeq

NP_415296.1. NC_000913.2.
YP_489048.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1R30	X-ray	3.40	A/B	2-346	[»]

ProteinModelPortal

P12996.

SMR

P12996. Positions 3-315.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-9220N.

IntAct

P12996. 3 interactions.

MINT

MINT-1292998.

STRING

511145.b0775.

Proteomic databases

PaxDb

P12996.

PRIDE

P12996.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73862; AAC73862; b0775.
BAE76362; BAE76362; BAE76362.

GeneID

12930955.
945370.

KEGG

ecj:Y75_p0748.
eco:b0775.

PATRIC

32116751. VBIEscCol129921_0801.

Organism-specific databases

EchoBASE

EB0116.

EcoGene

EG10118. bioB.

Phylogenomic databases

eggNOG

COG0502.

HOGENOM

HOG000239957.

KO

K01012.

OMA

RIMMPAS.

ProtClustDB

PRK15108.

Enzyme and pathway databases

BioCyc

EcoCyc:BIOTIN-SYN-MONOMER.
ECOL316407:JW0758-MONOMER.
MetaCyc:BIOTIN-SYN-MONOMER.

UniPathway

UPA00078; UER00162.

Gene expression databases

Genevestigator

P12996.

Family and domain databases

Gene3D

3.20.20.70. 1 hit.

HAMAP

MF_01694. BioB.

InterPro

IPR013785. Aldolase_TIM.
IPR010722. Biotin/thiamin_synth-assoc.
IPR002684. Biotin_synth/BioAB.
IPR024177. Biotin_synthase.
IPR006638. Elp3/MiaB/NifB.
IPR007197. rSAM.
[Graphical view]

Pfam

PF06968. BATS. 1 hit.
PF04055. Radical_SAM. 1 hit.
[Graphical view]

PIRSF

PIRSF001619. Biotin_synth. 1 hit.

SMART

SM00876. BATS. 1 hit.
SM00729. Elp3. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00433. bioB. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P12996.

Entry information

Entry name

BIOB_ECOLI

Accession

Primary (citable) accession number: P12996
Secondary accession number(s): Q2MBJ4

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1990
Last sequence update:	November 1, 1997
Last modified:	May 1, 2013
This is version 141 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program