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Gene |

Product(s) |

Expression|

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Standard Name	bioB
Gene Synonym(s)	ECK0764, b0775, JW0758, G8004^[1]^[2]
Product Desc.	biotin synthase^[2]^[3]; Component of biotin synthase^[2]^[3] Biotin synthase; dethiobiotin to biotin pathway; iron-sulfur enzyme^[4]
Product Synonyms(s)	biotin synthase^[1], B0775^[2]^[1], BioB^[2]^[1] , ECK0764, JW0758, b0775
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): bioBFCD^[2], OP00157
Regulation/Activity
Quick Links
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Notes

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Radical SAM superfamily. BioB contains two distinct Fe-S cluster binding sites, one site accommodates a [2Fe-2S](2+) cluster with partial noncysteinyl ligation, the other site accommodates a [4Fe-4S](2+,+) cluster that binds S-adenosylmethionine (SAM) at a unique Fe site of the [4Fe-4S](2+) cluster and undergoes O(2)-induced degradation via a distinct type of [2Fe-2S](2+) cluster intermediate.^[4]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	bioB
Mnemonic	Biotin
Synonyms	ECK0764, b0775, JW0758, G8004^[1]^[2]
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	17.43 minutes	MG1655: 808567..809607 <gbrowseImage> name=NC_000913:808567..809607 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 801970..803010 <gbrowseImage> name=NC_012967:801970..803010 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 711535..712575 <gbrowseImage> name=NC_012759:711535..712575 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 809766..810806 <gbrowseImage> name=NC_007779:809766..810806 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 862495..863535 <gbrowseImage> name=NC_010473:862495..863535 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
Coding Start (SO:0000323)	MG1655	808567	Edman degradation	PMID:8142361
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Description	Reference	Availability	Comments
bioBC97A		C97A	Total loss of activity			seeded from UniProt:P12996
bioBC188A		C188A	Total loss of activity			seeded from UniProt:P12996
bioBD155A		D155A	Total loss of activity			seeded from UniProt:P12996
bioBH152A		H152A	Weak activity			seeded from UniProt:P12996
bioBN153A		N153A	Total loss of activity			seeded from UniProt:P12996
bioBC128A		C128A	Total loss of activity			seeded from UniProt:P12996
bioBN151A		N151A	Total loss of activity			seeded from UniProt:P12996
bioBC60A		C60A	Total loss of activity			seeded from UniProt:P12996
bioBC53A		C53A	Total loss of activity			seeded from UniProt:P12996
bioBC57A		C57A	Total loss of activity			seeded from UniProt:P12996
ΔbioB (Keio:JW0758)	deletion	deletion		PMID:16738554	Shigen CGSC8319^[5]
bioB17					CGSC:7570
bioB102					CGSC:17107
bioB105					CGSC:37728
ΔbioB747::kan				PMID:16738554	CGSC:100196
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW0758	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCTCACCGCCCACGCTGGAC Primer 2:CCTAATGCTGCCGCGTTGTAATA
4H7	Kohara Phage	Genobase	PMID:3038334
3D4	Kohara Phage	Genobase	PMID:3038334
nadA57::Tn10	Linked marker	CAG12147 = CGSC7351^[5]	est. P1 cotransduction: 32% ^[6]
zbh-29::Tn10	Linked marker	CAG18493 = CGSC7353^[5]	est. P1 cotransduction: 64% ^[6] Synonyms:zbi-29::Tn10
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10118	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10118	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000114	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945370	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0116	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002644	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	BioB
Synonyms	biotin synthase^[1], B0775^[2]^[1], BioB^[2]^[1] , ECK0764, JW0758, b0775
Product description	biotin synthase^[2]^[3]; Component of biotin synthase^[2]^[3] Biotin synthase; dethiobiotin to biotin pathway; iron-sulfur enzyme^[4]
EC number (for enzymes)	2.8.1.6^[1]
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0004076	biotin synthase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01694	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004076	biotin synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002684	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004076	biotin synthase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010722	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004076	biotin synthase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.8.1.6	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005506	iron ion binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01694	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005506	iron ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0408	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009102	biotin biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01694	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009102	biotin biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002684	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009102	biotin biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010722	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009102	biotin biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0093	P	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051537	2 iron, 2 sulfur cluster binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0001	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051539	4 iron, 4 sulfur cluster binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0004	F	Seeded from EcoCyc (v14.0)	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	Notes	References	Evidence
Protein	Subunits of biotin synthase	could be indirect
Protein	dnaK		PMID:16606699	Experiment(s):EBI-1137925
Protein	nadE		PMID:16606699	Experiment(s):EBI-1137925
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc 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
Length	346
Mol. Wt	38.648 kDa
pI	5.3 (calculated)
Extinction coefficient	27,390 - 28,390 (calc based on 11 Y, 2 W, and 8 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	References
Domain	47..209	PF04055 Radical SAM superfamily	PMID:19920124
Domain	220..312	PF06968 Biotin and Thiamin Synthesis associated domain	PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=bioB taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16128743	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945370	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002644	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P12996	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10118	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10118	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945370	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000114	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0116	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MC4100	3.68E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	4948	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	898	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	7837	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
bioBFCD
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Figure courtesy of RegulonDB

</protect>

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:808547..808587 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b0775 (EcoliWiki Page)	NCBI GEO profiles for bioB
microarray	GenExpDB:b0775 (EcoliWiki Page)	Summary of data for bioB from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (808400..808638) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ07; Well:F12^[7]
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Notes

Accessions Related to bioB Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10118	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0116	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0775
EcoGene	EcoGene:EG10118	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000114	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002644	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Arabidopsis thaliana	AT2G43360 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q69U93 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YGR286C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPCC12352 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	BIOB	From SHIGELLACYC
E. coli O157	BIOB	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF04055 Radical SAM superfamily
Panther (EcoliWiki Page)	PTHR22976:SF1
Superfamily (EcoliWiki Page)	SUPERFAMILY:102114
Pfam (EcoliWiki Page)	PF06968 Biotin and Thiamin Synthesis associated domain
EcoCyc	EcoCyc:EG10118	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10118	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000114	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0116	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002644	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 ^1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

bioB:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to bioB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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