RegulonDB

Gene
Name:	gyrA
Synonym(s):	ECK2223, EG10423, b2231, hisW, nalA, nfxA, norA, parD
Genome position(nucleotides):	2336793 <-- 2339420
Strand:	reverse
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	54.0
External database links:

ASAP:	ABE-0007370
CGSC:	651
ECHOBASE:	EB0418
ECOLIHUB:	gyrA
OU-MICROARRAY:	b2231
STRING:	511145.b2231
COLOMBOS:	gyrA

Gene

Name:

gyrA

Synonym(s):

ECK2223, EG10423, b2231, hisW, nalA, nfxA, norA, parD

Genome position(nucleotides):

2336793 <-- 2339420

Strand:

reverse

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

54.0

External database links:

ASAP:

CGSC:

ECHOBASE:

ECOLIHUB:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

Comment

2 -> 875

SDLAREITPVNIEEELKSSYLDYAMSVIVGRALPDVRDGLKPVHRRVLYAMNVLGNDWNKAYKKSARVVGDVIGKYHPHGDSAVYDTIVRMAQPFSLRYMLVDGQGNFGSIDGDSAAAMRYTEIRLAKIAHELMADLEKETVDFVDNYDGTEKIPDVMPTKIPNLLVNGSSGIAVGMATNIPPHNLTEVINGCLAYIDDEDISIEGLMEHIPGPDFPTAAIINGRRGIEEAYRTGRGKVYIRARAEVEVDAKTGRETIIVHEIPYQVNKARLIEKIAELVKEKRVEGISALRDESDKDGMRIVIEVKRDAVGEVVLNNLYSQTQLQVSFGINMVALHHGQPKIMNLKDIIAAFVRHRREVVTRRTIFELRKARDRAHILEALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEFGVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAELLRILGSADRLMEVIREELELVREQFGDKRRTEITANSADINLEDLITQEDVVVTLSHQGYVKYQPLSEYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDHILCFSSRGRVYSMKVYQLPEATRGARGRPIVNLLPLEQDERITAILPVTEFEEGVKVFMATANGTVKKTVLTEFNRLRTAGKVAIKLVDGDELIGVDLTSGEDEVMLFSAEGKVVRFKESSVRAMGCNTTGVRGIRLGEGDKVVSLIVPRGDGAILTATQNGYGKRTAVAEYPTKSRATKGVISIKVTERNGLVVGAVQVDDCDQIMMITDAGTLVRTRVSEISIVGRNTQGVILIRTAEDENVVGLQRVAEPVDEEDLDTIDGSAAEGDDEIAPEVDVDDEPEEE

UniProt: DNA gyrase subunit A.

32 -> 32

UniProt: Nearly abolishes DNA supercoiling. Reduces quinolone-induced DNA cleavage and relaxation..

47 -> 47

UniProt: Nearly abolishes DNA supercoiling. Reduces quinolone-induced DNA cleavage. Slightly reduces DNA relaxation..

67 -> 67

UniProt: In PPA-10; quinolone-resistant..

78 -> 78

UniProt: Nearly abolishes DNA supercoiling. Reduces quinolone-induced DNA cleavage and DNA relaxation..

Type

Positions

Sequence

Comment

2 -> 875

UniProt: DNA gyrase subunit A.

32 -> 32

UniProt: Nearly abolishes DNA supercoiling. Reduces quinolone-induced DNA cleavage and relaxation..

47 -> 47

UniProt: Nearly abolishes DNA supercoiling. Reduces quinolone-induced DNA cleavage. Slightly reduces DNA relaxation..

67 -> 67

UniProt: In PPA-10; quinolone-resistant..

78 -> 78

UniProt: Nearly abolishes DNA supercoiling. Reduces quinolone-induced DNA cleavage and DNA relaxation..

80 -> 80

UniProt: Reduces DNA supercoiling. Slightly reduces quinolone-induced DNA cleavage. No effect on DNA relaxation..

81 -> 81

UniProt: In NAL-97; quinolone-resistant..

83 -> 83

UniProt: Resistant to fluoroquinolones..

84 -> 84

UniProt: In PPA-05; quinolone-resistant..

87 -> 87

D → G: present in a laboratory evolved strain of E. coli with high level resistance to norfloxacin

106 -> 106

UniProt: Resistant to fluoroquinolones..

462 -> 462

UniProt: In gyrA462; resistant to cytotoxic protein CcdB, but not to the quinoline antibiotic enoxacin, has no effect on DNA supercoiling. Does not interact with CcdB..

531 -> 841

EDLITQEDVVVTLSHQGYVKYQPLSEYEAQRRGGKGKSAARIKEEDFIDRLLVANTHDHILCFSSRGRVYSMKVYQLPEATRGARGRPIVNLLPLEQDERITAILPVTEFEEGVKVFMATANGTVKKTVLTEFNRLRTAGKVAIKLVDGDELIGVDLTSGEDEVMLFSAEGKVVRFKESSVRAMGCNTTGVRGIRLGEGDKVVSLIVPRGDGAILTATQNGYGKRTAVAEYPTKSRATKGVISIKVTERNGLVVGAVQVDDCDQIMMITDAGTLVRTRVSEISIVGRNTQGVILIRTAEDENVVGLQRVAE

UniProt: C-terminal domain (CTD); Sequence Annotation Type: region of interest.

538 -> 584

DVVVTLSHQGYVKYQPLSEYEAQRRGGKGKSAARIKEEDFIDRLLVA

560 -> 566

QRRGGKG

UniProt: GyrA-box; Sequence Annotation Type: short sequence motif.

588 -> 637

DHILCFSSRGRVYSMKVYQLPEATRGARGRPIVNLLPLEQDERITAILPV

646 -> 688

VFMATANGTVKKTVLTEFNRLRTAGKVAIKLVDGDELIGVDLT

678 -> 678

UniProt: In strain: 227..

692 -> 737

DEVMLFSAEGKVVRFKESSVRAMGCNTTGVRGIRLGEGDKVVSLIV

744 -> 789

ILTATQNGYGKRTAVAEYPTKSRATKGVISIKVTERNGLVVGAVQV

793 -> 839

DQIMMITDAGTLVRTRVSEISIVGRNTQGVILIRTAEDENVVGLQRV

798 -> 798

UniProt: In strain OV6; quinolone-resistant..

828 -> 828

UniProt: In strain: 227..

841 -> 875

EPVDEEDLDTIDGSAAEGDDEIAPEVDVDDEPEEE

UniProt: Disordered; Sequence Annotation Type: region of interest.

842 -> 856

PVDEEDLDTIDGSAA

UniProt: Gains ability to wrap DNA around itself in the absence of GyrB; holoenzyme gains ability to wrap DNA in the absence of ATP analogs, but reduces ATP-dependent supercoiling activity 50-fold, DNA is not as extensively negatively supercoiled, has 10-fold less ATP-independent negative supercoiled DNA relaxation activity, no change in ATPase activity of holoenzyme, no change in decatenation ability. Isolated CTD gains ability to wrap DNA around itself in the absence of GyrB, binds DNA better than wild-type CTD..

845 -> 875

EEDLDTIDGSAAEGDDEIAPEVDVDDEPEEE

UniProt: Acidic residues; Sequence Annotation Type: compositionally biased region.

854 -> 875

SAAEGDDEIAPEVDVDDEPEEE

UniProt: Isolated CTD gains ability to wrap DNA around itself in the absence of GyrB, binds DNA better than wild-type CTD..

Multifun Terms (GenProtEC)

2 - information transfer --> 2.1 - DNA related --> 2.1.1 - DNA replication

Gene Ontology Terms (GO)

cellular_component

GO:0120217 - DNA gyrase complex
GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0016020 - membrane
GO:0005694 - chromosome
GO:0009330 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex

molecular_function

GO:0003677 - DNA binding
GO:0003916 - DNA topoisomerase activity
GO:0005515 - protein binding
GO:0008094 - ATP-dependent activity, acting on DNA
GO:0016853 - isomerase activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0003918 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0042802 - identical protein binding
GO:0034335 - DNA negative supercoiling activity

biological_process

GO:0006259 - DNA metabolic process
GO:0006261 - DNA-templated DNA replication
GO:0006351 - transcription, DNA-templated
GO:0009410 - response to xenobiotic stimulus
GO:0046677 - response to antibiotic
GO:0006265 - DNA topological change
GO:2000104 - negative regulation of DNA-templated DNA replication

Transcriptional Regulation
	Display Regulation
Activated by:	CRP, CspA
Repressed by:	Fis

Transcriptional Regulation

Display Regulation

Activated by:

CRP, CspA

Repressed by:

Fis

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_2502	2338373	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_2503	2338375	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_2504	2338445	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_2505	2338825	reverse	nd	[RS-EPT-CBR]	[1]
promoter	TSS_2508 (cluster)	2339547	forward	nd	[RS-EPT-CBR]	[1]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_2502

2338373

reverse

[RS-EPT-CBR]

[1]

promoter

TSS_2503

2338375

reverse

[RS-EPT-CBR]

[1]

promoter

TSS_2504

2338445

reverse

[RS-EPT-CBR]

[1]

promoter

TSS_2505

2338825

reverse

[RS-EPT-CBR]

[1]

promoter

TSS_2508 (cluster)

2339547

forward

[RS-EPT-CBR]

[1]

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

Evidence

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

Reference(s)
[1] 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] 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.