Reviewed, UniProtKB/Swiss-Prot P0AES4 (GYRA_ECOLI)

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) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	875 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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.
Catalytic activity	ATP-dependent breakage, passage and rejoining of double-stranded DNA.
Subunit structure	Made up of two chains. The A chain is responsible for DNA breakage and rejoining; the B chain catalyzes ATP hydrolysis. The enzyme forms an A2B2 tetramer.
Miscellaneous	When the enzyme transiently cleaves DNA a phosphotyrosine bond is formed between the gyrA and DNA.
Sequence similarities	Belongs to the topoisomerase gyrA/parC subunit family.

Ontologies

Keywords
Biological process	Antibiotic resistance
Ligand	ATP-binding DNA-binding Nucleotide-binding
Molecular function	Isomerase Topoisomerase
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	DNA topological change Inferred from electronic annotation. Source: InterPro response to antibiotic Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	chromosome Inferred from electronic annotation. Source: InterPro cytoplasm Inferred from direct assay. Source: UniProtKB membrane Inferred from direct assay. Source: UniProtKB
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA topoisomerase (ATP-hydrolyzing) activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 875

875

DNA gyrase subunit A

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

83

1

S → A: Resistant to fluoroquinolones. Ref.12

Mutagenesis

106

1

Q → R: Resistant to fluoroquinolones. Ref.12

Secondary structure

1

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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

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)
	P0AES4-1 [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: 2828631] [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: 2830458] [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: 2834621] [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: 2548439] [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: 9205837] [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: 9278503] [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: 16738553] [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: 3029031] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-88.
[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: 3031051] [Abstract] Cited for: ACTIVE SITE TYR-122.
[10]	"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: 2168148] [Abstract] Cited for: VARIANTS QUINOLONE-RESISTANT.
[11]	"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: 1850972] [Abstract] Cited for: VARIANTS QUINOLONE-RESISTANT.
[12]	"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: 1850970] [Abstract] Cited for: MUTAGENESIS OF SER-83 AND GLN-106. Strain: K12.
[13]	"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: 9278055] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 30-522.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

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

AP_002828.1.
NP_416734.1.

3D structure databases

PDBPDBe

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	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P0AES4. 42 interactions.

2-D gel databases

SWISS-2DPAGE

P0AES4.

ECO2DBASE

D101.5. 6TH EDITION.

Genome annotation databases

GeneID

946614.

GenomeReviews

Gene locus JW2225 in contig AP009048_GR.
Gene locus b2231 in contig U00096_GR.

KEGG

ecj:JW2225.
eco:b2231.

Organism-specific databases

EchoBASE

EB0418.

EcoGene

EG10423. gyrA.

CMR

Search...

Phylogenomic databases

HOGENOM

P0AES4.

OMA

P0AES4. ELGNDWN.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10423-MON.

Family and domain databases

InterPro

IPR005743. GyrA.
IPR006691. GyrA/parC_pinwhl.
IPR002205. Topo_IIA_A/C.
IPR013758. Topo_IIA_A/C_ab.
IPR013757. Topo_IIA_A_a.
[Graphical view]

Gene3D

G3DSA:3.90.199.10. Topo_IIA_A/C_ab. 1 hit.
G3DSA:1.10.268.10. Topo_IIA_A_a. 1 hit.

Pfam

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

ProDom

PD000742. DNA_topoisoIV. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00434. TOP4c. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01063. gyrA. 1 hit.

ProtoNet

Search...

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:	June 16, 2009
This is version 38 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)