P05653 (GYRA_BACSU) 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:	cafB, nalA
Ordered Locus Names:	BSU00070

Organism

Bacillus subtilis (strain 168) [Reference proteome] [HAMAP]

Taxonomic identifier

224308 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus › Bacillus subtilis group › Bacillus subtilis › Bacillus subtilis subsp. subtilis

Protein attributes

Sequence length	821 AA.
Sequence status	Complete.
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 By similarity. HAMAP-Rule MF_01897
Catalytic activity	ATP-dependent breakage, passage and rejoining of double-stranded DNA. HAMAP-Rule MF_01897
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 By similarity.
Subcellular location	Cytoplasm Potential HAMAP-Rule MF_01897.
Sequence similarities	Belongs to the topoisomerase GyrA/ParC subunit family.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	ATP-binding DNA-binding Nucleotide-binding
Molecular function	Isomerase Topoisomerase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA topological change Inferred from Biological aspect of Ancestor. Source: RefGenome DNA-dependent DNA replication Inferred from Biological aspect of Ancestor. Source: RefGenome chromosome segregation Inferred from Biological aspect of Ancestor. Source: RefGenome
Cellular_component	chromosome Inferred from electronic annotation. Source: InterPro cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell 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 Biological aspect of Ancestor. Source: RefGenome
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 821

821

DNA gyrase subunit A HAMAP-Rule MF_01897

PRO_0000145221

Sites

Active site

123

1

O-(5'-phospho-DNA)-tyrosine intermediate By similarity

Secondary structure

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821

Helix Strand Turn

Details...

Turn

38 – 40

3

Helix

44 – 55

12

Beta strand

60 – 62

3

Beta strand

64 – 66

3

Helix

67 – 77

11

Helix

82 – 92

11

Turn

96 – 98

3

Beta strand

103 – 108

6

Beta strand

125 – 128

4

Helix

132 – 136

5

Beta strand

146 – 148

3

Beta strand

152 – 159

8

Helix

166 – 170

5

Beta strand

172 – 176

5

Beta strand

179 – 183

5

Helix

188 – 200

13

Helix

206 – 210

5

Beta strand

222 – 224

3

Helix

227 – 236

10

Beta strand

237 – 244

8

Beta strand

246 – 251

6

Beta strand

257 – 263

7

Helix

270 – 282

13

Beta strand

289 – 294

6

Beta strand

303 – 307

5

Helix

313 – 323

11

Beta strand

324 – 333

10

Beta strand

335 – 344

10

Helix

347 – 388

42

Helix

390 – 398

9

Helix

403 – 414

12

Helix

418 – 425

8

Helix

429 – 432

4

Helix

434 – 459

26

Helix

461 – 479

19

Beta strand

485 – 487

3

Sequences

	Sequence		Length	Mass (Da)
	P05653 [UniParc]. Last modified November 1, 1988. Version 1. Checksum: 717847A5F35FB857	FASTA	821	92,099
	10 20 30 40 50 60 MSEQNTPQVR EINISQEMRT SFLDYAMSVI VSRALPDVRD GLKPVHRRIL YAMNDLGMTS 70 80 90 100 110 120 DKPYKKSARI VGEVIGKYHP HGDSAVYESM VRMAQDFNYR YMLVDGHGNF GSVDGDSAAA 130 140 150 160 170 180 MRYTEARMSK ISMEILRDIT KDTIDYQDNY DGSEREPVVM PSRFPNLLVN GAAGIAVGMA 190 200 210 220 230 240 TNIPPHQLGE IIDGVLAVSE NPDITIPELM EVIPGPDFPT AGQILGRSGI RKAYESGRGS 250 260 270 280 290 300 ITIRAKAEIE QTSSGKERII VTELPYQVNK AKLIEKIADL VRDKKIEGIT DLRDESDRTG 310 320 330 340 350 360 MRIVIEIRRD ANANVILNNL YKQTALQTSF GINLLALVDG QPKVLTLKQC LEHYLDHQKV 370 380 390 400 410 420 VIRRRTAYEL RKAEARAHIL EGLRVALDHL DAVISLIRNS QTAEIARTGL IEQFSLTEKQ 430 440 450 460 470 480 AQAILDMRLQ RLTGLEREKI EEEYQSLVKL IAELKDILAN EYKVLEIIRE ELTEIKERFN 490 500 510 520 530 540 DERRTEIVTS GLETIEDEDL IERENIVVTL THNGYVKRLP ASTYRSQKRG GKGVQGMGTN 550 560 570 580 590 600 EDDFVEHLIS TSTHDTILFF SNKGKVYRAK GYEIPEYGRT AKGIPIINLL EVEKGEWINA 610 620 630 640 650 660 IIPVTEFNAE LYLFFTTKHG VSKRTSLSQF ANIRNNGLIA LSLREDDELM GVRLTDGTKQ 670 680 690 700 710 720 IIIGTKNGLL IRFPETDVRE MGRTAAGVKG ITLTDDDVVV GMEILEEESH VLIVTEKGYG 730 740 750 760 770 780 KRTPAEEYRT QSRGGKGLKT AKITENNGQL VAVKATKGEE DLMIITASGV LIRMDINDIS 790 800 810 820 ITGRVTQGVR LIRMAEEEHV ATVALVEKNE EDENEEEQEE V

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Structure and function of the region of the replication origin of the Bacillus subtilis chromosome. III. Nucleotide sequence of some 10,000 base pairs in the origin region." Moriya S., Ogasawara N., Yoshikawa H. Nucleic Acids Res. 13:2251-2265(1985) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Systematic sequencing of the 180 kilobase region of the Bacillus subtilis chromosome containing the replication origin." Ogasawara N., Nakai S., Yoshikawa H. DNA Res. 1:1-14(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: 168.
[3]	"The complete genome sequence of the Gram-positive bacterium Bacillus subtilis." Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V. , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A. Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 168.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X02369 Genomic DNA. Translation: CAA26222.1.
D26185 Genomic DNA. Translation: BAA05243.1.
AL009126 Genomic DNA. Translation: CAB11783.1.

PIR

F22930.

RefSeq

NP_387888.1. NC_000964.3.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4DDQ	X-ray	3.30	A/B/C/D/E/F	1-502	[»]

ProteinModelPortal

P05653.

SMR

P05653. Positions 11-809.

ModBase

Search...

Protein-protein interaction databases

IntAct

P05653. 4 interactions.

STRING

224308.BSU00070.

Proteomic databases

PaxDb

P05653.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

CAB11783; CAB11783; BSU00070.

GeneID

940002.

KEGG

bsu:BSU00070.

PATRIC

18971463. VBIBacSub10457_0008.

Organism-specific databases

GenoList

BSU00070. [Micado]

Phylogenomic databases

eggNOG

COG0188.

HOGENOM

HOG000076278.

KO

K02469.

OMA

IAQEDVV.

ProtClustDB

PRK05560.

Enzyme and pathway databases

BioCyc

BSUB:BSU00070-MONOMER.

Family and domain databases

Gene3D

3.30.1360.40. 1 hit.
3.90.199.10. 2 hits.

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.
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

P05653.

ChEMBL

CHEMBL4216.

Entry information

Entry name

GYRA_BACSU

Accession

Primary (citable) accession number: P05653

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1988
Last sequence update:	November 1, 1988
Last modified:	May 1, 2013
This is version 100 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program