P0AES4 (GYRA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA gyrase subunit A
EC=5.99.1.3

Gene names

Name:	gyrA
Synonyms:	hisW, nalA, parD
Ordered Locus Names:	b2231, JW2225

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	875 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings. Ref.11 Ref.12 Ref.14
Catalytic activity	ATP-dependent breakage, passage and rejoining of double-stranded DNA. Ref.11 Ref.12 Ref.14 Ref.21
Subunit structure	Heterotetramer, composed of two GyrA and two GyrB chains. Within the heterotetramer, GyrA contains the active site tyrosine that forms a covalent intermediate with the DNA, while GyrB contributes the cofactor binding sites and catalyzes ATP hydrolysis. Can form a 2:2 complex with toxin CcdB in which GyrA is inactive; rejuvenation of GyrA2CcdB2 is effected by CcdA. Ref.11 Ref.12 Ref.14 Ref.20
Subcellular location	Cytoplasm Potential HAMAP-Rule MF_01897.
Miscellaneous	When the enzyme transiently cleaves DNA a phosphotyrosine bond is formed between GyrA and DNA. This enzyme-DNA intermediate is the target of a number of topoisomerase poisons, including toxin CcdB. HAMAP-Rule MF_01897
Sequence similarities	Belongs to the topoisomerase GyrA/ParC subunit family.

Ontologies

Keywords
Biological process	Antibiotic resistance
Cellular component	Cytoplasm
Ligand	ATP-binding DNA-binding Nucleotide-binding
Molecular function	Isomerase Topoisomerase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	DNA topological change Inferred from mutant phenotype PubMed 6327603. Source: EcoliWiki DNA-dependent DNA replication Inferred from electronic annotation. Source: HAMAP chromosome segregation Inferred from Biological aspect of Ancestor. Source: RefGenome response to antibiotic Inferred from electronic annotation. Source: UniProtKB-KW response to drug Inferred from mutant phenotype PubMed 4208771PubMed 6178722PubMed 770163. Source: EcoliWiki transcription, DNA-dependent Inferred from direct assay PubMed 347446. Source: EcoliWiki
Cellular_component	chromosome Inferred from electronic annotation. Source: InterPro cytoplasm Inferred from direct assay PubMed 16858726. Source: UniProtKB membrane Inferred from direct assay PubMed 16858726. Source: UniProtKB nucleoid Inferred from Biological aspect of Ancestor. Source: RefGenome
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP DNA topoisomerase type II (ATP-hydrolyzing) activity Inferred from direct assay PubMed 368801. Source: EcoliWiki
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		2	EBI-547129,EBI-547129
gyrB	P0AES6	5	EBI-547129,EBI-541911
marR	P27245	2	EBI-547129,EBI-6409744

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed HAMAP-Rule MF_01897

Chain

2 – 875

874

DNA gyrase subunit A HAMAP-Rule MF_01897

PRO_0000145232

Sites

Active site

122

1

O-(5'-phospho-DNA)-tyrosine intermediate Ref.9

Natural variations

Natural variant

67

1

A → S in PPA-10; quinolone-resistant.

Natural variant

81

1

G → C in NAL-97; quinolone-resistant.

Natural variant

83

1

S → L in NAL-51, NAL-112, NAL-118 and NAL-119; quinolone-resistant.

Natural variant

83

1

S → W in PPA-18 and strain 227; quinolone-resistant.

Natural variant

84

1

A → P in PPA-05; quinolone-resistant.

Natural variant

87

1

D → N in NAL-113 and KL-16; quinolone-resistant.

Natural variant

87

1

D → V in strain: 202; quinolone-resistant.

Natural variant

106

1

Q → H in NAL-89; quinolone-resistant.

Natural variant

678

1

D → E in strain: 227.

Natural variant

798

1

I → IMMI in KL-16; quinolone-resistant.

Natural variant

828

1

A → S in strain: 227.

Experimental info

Mutagenesis

32

1

R → A or Q: Nearly abolishes DNA supercoiling. Reduces DNA cleavage and relaxation. Ref.11

Mutagenesis

47

1

R → Q: Nearly abolishes DNA supercoiling. Reduces DNA cleavage. Slightly reduces DNA relaxation. Ref.11

Mutagenesis

78

1

H → A: Nearly abolishes DNA supercoiling. Reduces DNA cleavage and DNA relaxation. Ref.11

Mutagenesis

80

1

H → A: Reduces DNA supercoiling. Slightly reduces DNA cleavage. No effect on DNA relaxation. Ref.11

Mutagenesis

83

1

S → A: Resistant to fluoroquinolones. Ref.17

Mutagenesis

106

1

Q → R: Resistant to fluoroquinolones. Ref.17

Mutagenesis

462

1

R → C 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. Ref.18 Ref.19

Secondary structure

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875

Helix Strand Turn

Details...

Turn

31 – 33

3

Turn

37 – 39

3

Helix

43 – 54

12

Beta strand

59 – 61

3

Helix

66 – 76

11

Helix

82 – 91

10

Turn

95 – 97

3

Beta strand

102 – 107

6

Turn

120 – 122

3

Beta strand

124 – 127

4

Helix

131 – 134

4

Turn

136 – 141

6

Beta strand

145 – 147

3

Beta strand

151 – 158

8

Helix

165 – 169

5

Beta strand

171 – 173

3

Beta strand

180 – 182

3

Helix

187 – 199

13

Helix

205 – 208

4

Turn

209 – 211

3

Helix

227 – 235

9

Beta strand

236 – 243

8

Beta strand

245 – 249

5

Beta strand

258 – 263

6

Helix

270 – 281

12

Turn

282 – 284

3

Beta strand

292 – 294

3

Beta strand

298 – 300

3

Beta strand

303 – 305

3

Helix

314 – 323

10

Beta strand

327 – 333

7

Beta strand

335 – 338

4

Beta strand

341 – 344

4

Helix

347 – 388

42

Helix

390 – 399

10

Beta strand

400 – 402

3

Helix

403 – 412

10

Helix

419 – 421

3

Beta strand

441 – 449

9

Helix

452 – 459

8

Helix

463 – 466

4

Helix

468 – 493

26

Helix

495 – 513

19

Beta strand

519 – 521

3

Beta strand

538 – 544

7

Beta strand

547 – 553

7

Beta strand

578 – 585

8

Beta strand

589 – 594

6

Beta strand

597 – 603

7

Helix

604 – 606

3

Beta strand

612 – 614

3

Helix

619 – 621

3

Beta strand

631 – 638

8

Beta strand

645 – 650

6

Beta strand

653 – 659

7

Helix

660 – 663

4

Beta strand

671 – 674

4

Beta strand

682 – 688

7

Beta strand

693 – 698

6

Beta strand

701 – 707

7

Helix

708 – 710

3

Beta strand

732 – 736

5

Beta strand

743 – 748

6

Beta strand

751 – 756

6

Helix

758 – 760

3

Beta strand

771 – 774

4

Turn

778 – 780

3

Beta strand

782 – 789

8

Beta strand

794 – 801

8

Beta strand

804 – 808

5

Helix

809 – 811

3

Beta strand

833 – 838

6

Sequences

	Sequence		Length	Mass (Da)
	P0AES4 [UniParc]. Last modified December 20, 2005. Version 1. Checksum: 3FD5BD52A5969069	FASTA	875	96,964
	10 20 30 40 50 60 MSDLAREITP VNIEEELKSS YLDYAMSVIV GRALPDVRDG LKPVHRRVLY AMNVLGNDWN 70 80 90 100 110 120 KAYKKSARVV GDVIGKYHPH GDSAVYDTIV RMAQPFSLRY MLVDGQGNFG SIDGDSAAAM 130 140 150 160 170 180 RYTEIRLAKI AHELMADLEK ETVDFVDNYD GTEKIPDVMP TKIPNLLVNG SSGIAVGMAT 190 200 210 220 230 240 NIPPHNLTEV INGCLAYIDD EDISIEGLME HIPGPDFPTA AIINGRRGIE EAYRTGRGKV 250 260 270 280 290 300 YIRARAEVEV DAKTGRETII VHEIPYQVNK ARLIEKIAEL VKEKRVEGIS ALRDESDKDG 310 320 330 340 350 360 MRIVIEVKRD AVGEVVLNNL YSQTQLQVSF GINMVALHHG QPKIMNLKDI IAAFVRHRRE 370 380 390 400 410 420 VVTRRTIFEL RKARDRAHIL EALAVALANI DPIIELIRHA PTPAEAKTAL VANPWQLGNV 430 440 450 460 470 480 AAMLERAGDD AARPEWLEPE FGVRDGLYYL TEQQAQAILD LRLQKLTGLE HEKLLDEYKE 490 500 510 520 530 540 LLDQIAELLR ILGSADRLME VIREELELVR EQFGDKRRTE ITANSADINL EDLITQEDVV 550 560 570 580 590 600 VTLSHQGYVK YQPLSEYEAQ RRGGKGKSAA RIKEEDFIDR LLVANTHDHI LCFSSRGRVY 610 620 630 640 650 660 SMKVYQLPEA TRGARGRPIV NLLPLEQDER ITAILPVTEF EEGVKVFMAT ANGTVKKTVL 670 680 690 700 710 720 TEFNRLRTAG KVAIKLVDGD ELIGVDLTSG EDEVMLFSAE GKVVRFKESS VRAMGCNTTG 730 740 750 760 770 780 VRGIRLGEGD KVVSLIVPRG DGAILTATQN GYGKRTAVAE YPTKSRATKG VISIKVTERN 790 800 810 820 830 840 GLVVGAVQVD DCDQIMMITD AGTLVRTRVS EISIVGRNTQ GVILIRTAED ENVVGLQRVA 850 860 870 EPVDEEDLDT IDGSAAEGDD EIAPEVDVDD EPEEE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and sequencing of the Escherichia coli gyrA gene coding for the A subunit of DNA gyrase." Swanberg S.L., Wang J.C. J. Mol. Biol. 197:729-736(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Quinolone-resistant mutations of the gyrA gene of Escherichia coli." Yoshida H., Kojima T., Yamagishi J., Nakamura S. Mol. Gen. Genet. 211:1-7(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12 / KL16.
[3]	"The parD- mutant of Escherichia coli also carries a gyrAam mutation. The complete sequence of gyrA." Hussain K., Elliott E.J., Salmond G.P.C. Mol. Microbiol. 1:259-273(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: OV6.
[4]	"Cloning and characterization of a DNA gyrase A gene from Escherichia coli that confers clinical resistance to 4-quinolones." Cullen M.E., Wyke A.W., Kuroda R., Fisher L.M. Antimicrob. Agents Chemother. 33:886-894(1989) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: 227.
[5]	"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T. DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	"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.
[7]	"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.
[8]	"Fusions of the Escherichia coli gyrA and gyrB control regions to the galactokinase gene are inducible by coumermycin treatment." Menzel R., Gellert M. J. Bacteriol. 169:1272-1278(1987) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-88, PARTIAL PROTEIN SEQUENCE.
[9]	"Mapping the active site tyrosine of Escherichia coli DNA gyrase." Horowitz D.S., Wang J.C. J. Biol. Chem. 262:5339-5344(1987) [PubMed] [Europe PMC] [Abstract] Cited for: ACTIVE SITE TYR-122.
[10]	"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.
[11]	"Identification of four GyrA residues involved in the DNA breakage-reunion reaction of DNA gyrase." Hockings S.C., Maxwell A. J. Mol. Biol. 318:351-359(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, MUTAGENESIS OF ARG-32; ARG-47; HIS-78 AND HIS-80.
[12]	"DNA gyrase requires DNA for effective two-site coordination of divalent metal ions: further insight into the mechanism of enzyme action." Sissi C., Chemello A., Vazquez E., Mitchenall L.A., Maxwell A., Palumbo M. Biochemistry 47:8538-8545(2008) [PubMed] [Europe PMC] [Abstract] Cited for: CATALYTIC ACTIVITY, FUNCTION, COFACTOR, SUBUNIT.
[13]	"A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias." Ruthenburg A.J., Graybosch D.M., Huetsch J.C., Verdine G.L. J. Biol. Chem. 280:26177-26184(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 535-841.
[14]	"A crystal structure of the bifunctional antibiotic simocyclinone D8, bound to DNA gyrase." Edwards M.J., Flatman R.H., Mitchenall L.A., Stevenson C.E., Le T.B., Clarke T.A., McKay A.R., Fiedler H.P., Buttner M.J., Lawson D.M., Maxwell A. Science 326:1415-1418(2009) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.62 ANGSTROMS) OF 2-523 IN COMPLEX WITH ANTIBIOTIC SIMOCYCLINONE D8, CATALYTIC ACTIVITY, SUBUNIT, FUNCTION.
[15]	"Quinolone resistance-determining region in the DNA gyrase gyrA gene of Escherichia coli." Yoshida H., Bogaki M., Nakamura M., Nakamura S. Antimicrob. Agents Chemother. 34:1271-1272(1990) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANTS QUINOLONE-RESISTANT.
[16]	"4-quinolone resistance mutations in the DNA gyrase of Escherichia coli clinical isolates identified by using the polymerase chain reaction." Oram M., Fisher L.M. Antimicrob. Agents Chemother. 35:387-389(1991) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANTS QUINOLONE-RESISTANT.
[17]	"Novel quinolone resistance mutations of the Escherichia coli DNA gyrase A protein: enzymatic analysis of the mutant proteins." Hallett P., Maxwell A. Antimicrob. Agents Chemother. 35:335-340(1991) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF SER-83 AND GLN-106. Strain: K12.
[18]	"Cell killing by the F plasmid CcdB protein involves poisoning of DNA-topoisomerase II complexes." Bernard P., Couturier M. J. Mol. Biol. 226:735-745(1992) [PubMed] [Europe PMC] [Abstract] Cited for: INHIBITION BY TOXIN PROTEIN CCDB, MUTAGENESIS OF ARG-462. Strain: K12.
[19]	"The F plasmid CcdB protein induces efficient ATP-dependent DNA cleavage by gyrase." Bernard P., Kezdy K.E., Van Melderen L., Steyaert J., Wyns L., Pato M.L., Higgins P.N., Couturier M. J. Mol. Biol. 234:534-541(1993) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF ARG-462.
[20]	"Partner switching mechanisms in inactivation and rejuvenation of Escherichia coli DNA gyrase by F plasmid proteins LetD (CcdB) and LetA (CcdA)." Maki S., Takiguchi S., Horiuchi T., Sekimizu K., Miki T. J. Mol. Biol. 256:473-482(1996) [PubMed] [Europe PMC] [Abstract] Cited for: INHIBITION BY TOXIN PROTEIN CCDB, REJUVENATION BY CCDA, SUBUNIT.
[21]	"Crystal structure of the breakage-reunion domain of DNA gyrase." Cabral J.H., Jackson A.P., Smith C.V., Shikotra N., Maxwell A., Liddington R.C. Nature 388:903-906(1997) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 30-522, CATALYTIC ACTIVITY.
[22]	"Molecular basis of gyrase poisoning by the addiction toxin CcdB." Dao-Thi M.H., Van Melderen L., De Genst E., Afif H., Buts L., Wyns L., Loris R. J. Mol. Biol. 348:1091-1102(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 363-494 IN COMPLEX WITH CCBD.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X06373 Genomic DNA. Translation: CAA29676.1.
X06744 Genomic DNA. Translation: CAA29919.1.
M15631 Genomic DNA. Translation: AAA23948.1.
U00096 Genomic DNA. Translation: AAC75291.1.
AP009048 Genomic DNA. Translation: BAA16048.1.
Y00544 Genomic DNA. Translation: CAA68611.1.

PIR

ITECAP. S02340.

RefSeq

NP_416734.1. NC_000913.2.
YP_490470.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1AB4	X-ray	2.80	A	30-522	[»]
1X75	X-ray	2.80	A/B	363-494	[»]
1ZI0	X-ray	2.60	A/B	535-841	[»]
2Y3P	X-ray	2.62	A/B	2-523	[»]
3NUH	X-ray	3.10	A	1-525	[»]
4ELY	X-ray	1.93	A/B	363-497	[»]

ProteinModelPortal

P0AES4.

SMR

P0AES4. Positions 13-522, 535-841.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-36179N.

IntAct

P0AES4. 51 interactions.

MINT

MINT-201682.

STRING

511145.b2231.

2D gel databases

SWISS-2DPAGE

P0AES4.

Proteomic databases

PaxDb

P0AES4.

PRIDE

P0AES4.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75291; AAC75291; b2231.
BAA16048; BAA16048; BAA16048.

GeneID

12933138.
946614.

KEGG

ecj:Y75_p2193.
eco:b2231.

PATRIC

32119821. VBIEscCol129921_2320.

Organism-specific databases

EchoBASE

EB0418.

EcoGene

EG10423. gyrA.

Phylogenomic databases

eggNOG

COG0188.

HOGENOM

HOG000076278.

KO

K02469.

OMA

IAQEDVV.

ProtClustDB

PRK05560.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10423-MONOMER.
ECOL316407:JW2225-MONOMER.
MetaCyc:EG10423-MONOMER.

Gene expression databases

Genevestigator

P0AES4.

Family and domain databases

Gene3D

1.10.268.10. 1 hit.
3.30.1360.40. 1 hit.
3.90.199.10. 1 hit.

HAMAP

MF_01897. GyrA.

InterPro

IPR024946. Arg_repress_C-like.
IPR005743. GyrA.
IPR006691. GyrA/parC_pinwhl.
IPR002205. Topo_IIA_A/C.
IPR013758. Topo_IIA_A/C_ab.
IPR013757. Topo_IIA_A_a.
IPR013760. Topo_IIA_like_dom.
[Graphical view]

Pfam

PF03989. DNA_gyraseA_C. 6 hits.
PF00521. DNA_topoisoIV. 1 hit.
[Graphical view]

SMART

SM00434. TOP4c. 1 hit.
[Graphical view]

SUPFAM

SSF56719. Topo_IIA_cen. 1 hit.

TIGRFAMs

TIGR01063. gyrA. 1 hit.

ProtoNet

Search...

Other

BindingDB

P0AES4.

ChEMBL

CHEMBL1858.

EvolutionaryTrace

P0AES4.

Entry information

Entry name

GYRA_ECOLI

Accession

Primary (citable) accession number: P0AES4
Secondary accession number(s): P09097

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 20, 2005
Last sequence update:	December 20, 2005
Last modified:	May 1, 2013
This is version 77 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program