RegulonDB

Gene
Name:	cyoB
Synonym(s):	ECK0425, EG10179, b0431
Genome position(nucleotides):	448650 <-- 450641
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	52.96
External database links:

ASAP:	ABE-0001493
CGSC:	30997
ECHOBASE:	EB0176
ECOLIHUB:	cyoB
MIM:	550500
MIM:	535000
MIM:	220110
MIM:	114500
MIM:	500008
OU-MICROARRAY:	b0431
STRING:	511145.b0431
COLOMBOS:	cyoB

Gene

Name:

cyoB

Synonym(s):

ECK0425, EG10179, b0431

Genome position(nucleotides):

448650 <-- 450641

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

52.96

External database links:

ASAP:

CGSC:

ECHOBASE:

ECOLIHUB:

MIM:

MIM:

MIM:

MIM:

MIM:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

Comment

17 -> 35

VMVTIAGIILGGLALVGLI

UniProt: Helical; Name=I.

53 -> 80

DHKRLGIMYIIVAIVMLLRGFADAIMMR

UniProt: Helical; Name=II.

54 -> 54

UniProt: 50% quinol oxidase activity..

55 -> 55

UniProt: No effect..

56 -> 504

RLGIMYIIVAIVMLLRGFADAIMMRSQQALASAGEAGFLPPHHYDQIFTAHGVIMIFFVAMPFVIGLMNLVVPLQIGARDVAFPFLNNLSFWFTVVGVILVNVSLGVGEFAQTGWLAYPPLSGIEYSPGVGVDYWIWSLQLSGIGTTLTGINFFVTILKMRAPGMTMFKMPVFTWASLCANVLIIASFPILTVTVALLTLDRYLGTHFFTNDMGGNMMMYINLIWAWGHPEVYILILPVFGVFSEIAATFSRKRLFGYTSLVWATVCITVLSFIVWLHHFFTMGAGANVNAFFGITTMIIAIPTGVKIFNWLFTMYQGRIVFHSAMLWTIGFIVTFSVGGMTGVLLAVPGADFVLHNSLFLIAHFHNVIIGGVVFGCFAGMTYWWPKAFGFKLNETWGKRAFWFWIIGFFVAFMPLYALGFMGMTRRLSQQIDPQFHTMLMIAASGAVL

Type

Positions

Sequence

Comment

17 -> 35

VMVTIAGIILGGLALVGLI

UniProt: Helical; Name=I.

53 -> 80

DHKRLGIMYIIVAIVMLLRGFADAIMMR

UniProt: Helical; Name=II.

54 -> 54

UniProt: 50% quinol oxidase activity..

55 -> 55

UniProt: No effect..

56 -> 504

71 -> 71

UniProt: Abolishes quinol oxidase activity..

75 -> 75

UniProt: Abolishes quinol oxidase activity..

80 -> 80

UniProt: Abolishes quinol oxidase activity..

96 -> 132

PHHYDQIFTAHGVIMIFFVAMPFVIGLMNLVVPLQIG

UniProt: Helical; Name=III.

98 -> 98

UniProt: Abolishes enzyme activity..

101 -> 101

UniProt: Reduces quinol oxidase activity by 75%, decreased affinity for ubiquinol-1..

102 -> 102

UniProt: No quinol oxidase activity..

106 -> 106

UniProt: 2% quinol oxidase activity, loss of heme b, loss of heme o, loss of Cu(B)..

135 -> 135

UniProt: Abolishes quinol oxidase activity..

138 -> 161

FPFLNNLSFWFTVVGVILVNVSLG

UniProt: Helical; Name=IV.

173 -> 173

UniProt: No effect..

185 -> 215

VGVDYWIWSLQLSGIGTTLTGINFFVTILKM

UniProt: Helical; Name=V.

188 -> 188

UniProt: No effect..

225 -> 260

MPVFTWASLCANVLIIASFPILTVTVALLTLDRYLG

UniProt: Helical; Name=VI.

256 -> 256

UniProt: No effect..

257 -> 257

UniProt: Abolishes quinol oxidase activity..

271 -> 307

NMMMYINLIWAWGHPEVYILILPVFGVFSEIAATFSR

UniProt: Helical; Name=VII.

284 -> 284

UniProt: 1% quinol oxidase activity, loss of heme o..

286 -> 286

UniProt: Great decrease in quinol oxidase activity..

288 -> 288

UniProt: Great decrease in activity, 100-fold decrease in heme b-to-heme o electron transfer..

312 -> 326

GYTSLVWATVCITVL

UniProt: Helical; Name=VIII.

333 -> 333

UniProt: 2% quinol oxidase activity, loss of Cu(B)..

334 -> 334

UniProt: 1% quinol oxidase activity, loss of Cu(B)..

341 -> 369

GANVNAFFGITTMIIAIPTGVKIFNWLFT

UniProt: Helical; Name=IX.

362 -> 362

UniProt: Abolishes quinol oxidase activity, 100-fold decrease in heme b-to-heme o electron transfer..

378 -> 409

HSAMLWTIGFIVTFSVGGMTGVLLAVPGADFV

UniProt: Helical; Name=X.

407 -> 407

UniProt: Abolishes quinol oxidase activity..

411 -> 411

UniProt: 50% quinol oxidase activity..

413 -> 445

SLFLIAHFHNVIIGGVVFGCFAGMTYWWPKAFG

UniProt: Helical; Name=XI.

419 -> 419

UniProt: 3% quinol oxidase activity, loss of heme o, loss of Cu(B)..

421 -> 421

UniProt: 1% quinol oxidase activity, loss of heme b, some loss of Cu(B)..

449 -> 477

NETWGKRAFWFWIIGFFVAFMPLYALGFM

UniProt: Helical; Name=XII.

481 -> 481

UniProt: No effect..

482 -> 482

UniProt: No effect..

490 -> 521

QFHTMLMIAASGAVLIALGILCLVIQMYVSIR

UniProt: Helical; Name=XIII.

540 -> 540

UniProt: Abolishes quinol oxidase activity..

588 -> 606

NSGAGIVIAAFSTIFGFAM

UniProt: Helical; Name=XIV.

614 -> 632

AIVGFAGMIITWIVKSFDE

UniProt: Helical; Name=XV.

Multifun Terms (GenProtEC)

1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.6 - aerobic respiration

1 - metabolism --> 1.4 - energy production/transport --> 1.4.2 - electron acceptors

4 - transport --> 4.3 - Primary Active Transporters --> 4.3.D - Oxidoreduction-driven Active Transporters

6 - cell structure --> 6.1 - membrane

Gene Ontology Terms (GO)

cellular_component

GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane
GO:0070469 - respirasome
GO:0009319 - cytochrome o ubiquinol oxidase complex

molecular_function

GO:0005507 - copper ion binding
GO:0005515 - protein binding
GO:0009055 - electron transfer activity
GO:0015453 - oxidoreduction-driven active transmembrane transporter activity
GO:0046872 - metal ion binding
GO:0015078 - proton transmembrane transporter activity
GO:0004129 - cytochrome-c oxidase activity
GO:0009486 - cytochrome bo3 ubiquinol oxidase activity
GO:0016682 - oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
GO:0020037 - heme binding
GO:0048039 - ubiquinone binding

biological_process

GO:0006811 - ion transport
GO:0009060 - aerobic respiration
GO:0015990 - electron transport coupled proton transport
GO:0019646 - aerobic electron transport chain
GO:0022904 - respiratory electron transport chain

Transcriptional Regulation
	Display Regulation
Activated by:	CRP, CusR, GadE, Fis
Repressed by:	Fur, FNR, HprR, Cra, ArcA, PdhR

Transcriptional Regulation

Display Regulation

Activated by:

CRP, CusR, GadE, Fis

Repressed by:

Fur, FNR, HprR, Cra, ArcA, PdhR

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	cyoEp3	447770	reverse	nd	[COMP-AINF]	[7]
promoter	TSS_547	448138	reverse	nd	[RS-EPT-CBR]	[8]
promoter	TSS_548 (cluster)	448146	reverse	nd	[RS-EPT-CBR]	[8]
promoter	TSS_549	448244	reverse	nd	[RS-EPT-CBR]	[8]
promoter	TSS_550 (cluster)	448247	reverse	nd	[RS-EPT-CBR]	[8]
promoter	TSS_551	448549	reverse	nd	[RS-EPT-CBR]	[8]
promoter	TSS_552	448681	reverse	nd	[RS-EPT-CBR]	[8]
promoter	TSS_553	449899	reverse	nd	[RS-EPT-CBR]	[8]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

cyoEp3

447770

reverse

[COMP-AINF]

[7]

promoter

TSS_547

448138

reverse

[RS-EPT-CBR]

[8]

promoter

TSS_548 (cluster)

448146

reverse

[RS-EPT-CBR]

[8]

promoter

TSS_549

448244

reverse

[RS-EPT-CBR]

[8]

promoter

TSS_550 (cluster)

448247

reverse

[RS-EPT-CBR]

[8]

promoter

TSS_551

448549

reverse

[RS-EPT-CBR]

[8]

promoter

TSS_552

448681

reverse

[RS-EPT-CBR]

[8]

promoter

TSS_553

449899

reverse

[RS-EPT-CBR]

[8]

Evidence
[COMP-AINF] Inferred computationally without human oversight
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Evidence

[COMP-AINF] Inferred computationally without human oversight

[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Barker PD., Freund SM., 1996, Bis-methionine ligation to heme iron in mutants of cytochrome b562. 2. Characterization by NMR of heme-ligand interactions., Biochemistry 35(42):13627-35
[2] Barker PD., Nerou EP., Cheesman MR., Thomson AJ., de Oliveira P., Hill HA., 1996, Bis-methionine ligation to heme iron in mutants of cytochrome b562. 1. Spectroscopic and electrochemical characterization of the electronic properties., Biochemistry 35(42):13618-26
[3] Kobayashi K., Tagawa S., Mogi T., 2009, Electron transfer processes in subunit I mutants of cytochrome bo quinol oxidase in Escherichia coli., Biosci Biotechnol Biochem 73(7):1599-603
[4] Lin MT., Samoilova RI., Gennis RB., Dikanov SA., 2008, Identification of the nitrogen donor hydrogen bonded with the semiquinone at the Q(H) site of the cytochrome bo3 from Escherichia coli., J Am Chem Soc 130(47):15768-9
[5] Melin F., Sabuncu S., Choi SK., Leprince A., Gennis RB., Hellwig P., 2018, Role of the tightly bound quinone for the oxygen reaction of cytochrome bo₃ oxidase from Escherichia coli., FEBS Lett 592(20):3380-3387
[6] Thomas JW., Lemieux LJ., Alben JO., Gennis RB., 1993, Site-directed mutagenesis of highly conserved residues in helix VIII of subunit I of the cytochrome bo ubiquinol oxidase from Escherichia coli: an amphipathic transmembrane helix that may be important in conveying protons to the binuclear center., Biochemistry 32(41):11173-80
[7] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78
[8] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

Reference(s)

[1] Barker PD., Freund SM., 1996, Bis-methionine ligation to heme iron in mutants of cytochrome b562. 2. Characterization by NMR of heme-ligand interactions., Biochemistry 35(42):13627-35

[2] Barker PD., Nerou EP., Cheesman MR., Thomson AJ., de Oliveira P., Hill HA., 1996, Bis-methionine ligation to heme iron in mutants of cytochrome b562. 1. Spectroscopic and electrochemical characterization of the electronic properties., Biochemistry 35(42):13618-26

[3] Kobayashi K., Tagawa S., Mogi T., 2009, Electron transfer processes in subunit I mutants of cytochrome bo quinol oxidase in Escherichia coli., Biosci Biotechnol Biochem 73(7):1599-603

[4] Lin MT., Samoilova RI., Gennis RB., Dikanov SA., 2008, Identification of the nitrogen donor hydrogen bonded with the semiquinone at the Q(H) site of the cytochrome bo3 from Escherichia coli., J Am Chem Soc 130(47):15768-9

[5] Melin F., Sabuncu S., Choi SK., Leprince A., Gennis RB., Hellwig P., 2018, Role of the tightly bound quinone for the oxygen reaction of cytochrome bo₃ oxidase from Escherichia coli., FEBS Lett 592(20):3380-3387

[6] Thomas JW., Lemieux LJ., Alben JO., Gennis RB., 1993, Site-directed mutagenesis of highly conserved residues in helix VIII of subunit I of the cytochrome bo ubiquinol oxidase from Escherichia coli: an amphipathic transmembrane helix that may be important in conveying protons to the binuclear center., Biochemistry 32(41):11173-80

[7] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

[8] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.