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P05653

- GYRA_BACSU

UniProt

P05653 - GYRA_BACSU

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Protein

DNA gyrase subunit A

Gene

gyrA

Organism
Bacillus subtilis (strain 168)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli

Functioni

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.UniRule annotation

Catalytic activityi

ATP-dependent breakage, passage and rejoining of double-stranded DNA.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei123 – 1231O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. DNA binding Source: UniProtKB-HAMAP
  3. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: RefGenome

GO - Biological processi

  1. ATP catabolic process Source: GOC
  2. chromosome segregation Source: RefGenome
  3. DNA topological change Source: RefGenome
  4. DNA unwinding involved in DNA replication Source: RefGenome
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

ATP-binding, DNA-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciBSUB:BSU00070-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit AUniRule annotation (EC:5.99.1.3UniRule annotation)
Gene namesi
Name:gyrAUniRule annotation
Synonyms:cafB, nalA
Ordered Locus Names:BSU00070
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570: Chromosome

Organism-specific databases

GenoListiBSU00070. [Micado]

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. chromosome Source: InterPro
  2. cytoplasm Source: UniProtKB-HAMAP
  3. DNA topoisomerase complex (ATP-hydrolyzing) Source: RefGenome
  4. nucleoid Source: RefGenome
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 821821DNA gyrase subunit APRO_0000145221Add
BLAST

Proteomic databases

PaxDbiP05653.

Interactioni

Subunit structurei

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.UniRule annotation

Protein-protein interaction databases

IntActiP05653. 5 interactions.
MINTiMINT-8366974.
STRINGi224308.BSU00070.

Structurei

Secondary structure

1
821
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni38 – 403Combined sources
Helixi44 – 5512Combined sources
Beta strandi60 – 623Combined sources
Beta strandi64 – 663Combined sources
Helixi67 – 7711Combined sources
Helixi82 – 9211Combined sources
Turni96 – 983Combined sources
Beta strandi103 – 1086Combined sources
Beta strandi125 – 1284Combined sources
Helixi132 – 1365Combined sources
Beta strandi146 – 1483Combined sources
Beta strandi152 – 1598Combined sources
Helixi166 – 1705Combined sources
Beta strandi172 – 1765Combined sources
Beta strandi179 – 1835Combined sources
Helixi188 – 20013Combined sources
Helixi206 – 2105Combined sources
Beta strandi222 – 2243Combined sources
Helixi227 – 23610Combined sources
Beta strandi237 – 2448Combined sources
Beta strandi246 – 2516Combined sources
Beta strandi257 – 2637Combined sources
Helixi270 – 28213Combined sources
Beta strandi289 – 2946Combined sources
Beta strandi303 – 3075Combined sources
Helixi313 – 32311Combined sources
Beta strandi324 – 33310Combined sources
Beta strandi335 – 34410Combined sources
Helixi347 – 38842Combined sources
Helixi390 – 3989Combined sources
Helixi403 – 41412Combined sources
Helixi418 – 4258Combined sources
Helixi429 – 4324Combined sources
Helixi434 – 45926Combined sources
Helixi461 – 47919Combined sources
Beta strandi485 – 4873Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4DDQX-ray3.30A/B/C/D/E/F1-502[»]
ProteinModelPortaliP05653.
SMRiP05653. Positions 11-809.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the topoisomerase GyrA/ParC subunit family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0188.
HOGENOMiHOG000076278.
InParanoidiP05653.
KOiK02469.
OMAiQTVFGIN.
OrthoDBiEOG661H5V.
PhylomeDBiP05653.

Family and domain databases

Gene3Di3.30.1360.40. 1 hit.
3.90.199.10. 2 hits.
HAMAPiMF_01897. GyrA.
InterProiIPR024946. 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]
PfamiPF03989. DNA_gyraseA_C. 6 hits.
PF00521. DNA_topoisoIV. 1 hit.
[Graphical view]
SMARTiSM00434. TOP4c. 1 hit.
[Graphical view]
SUPFAMiSSF56719. SSF56719. 1 hit.
TIGRFAMsiTIGR01063. gyrA. 1 hit.

Sequencei

Sequence statusi: Complete.

P05653-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSEQNTPQVR EINISQEMRT SFLDYAMSVI VSRALPDVRD GLKPVHRRIL
60 70 80 90 100
YAMNDLGMTS DKPYKKSARI VGEVIGKYHP HGDSAVYESM VRMAQDFNYR
110 120 130 140 150
YMLVDGHGNF GSVDGDSAAA MRYTEARMSK ISMEILRDIT KDTIDYQDNY
160 170 180 190 200
DGSEREPVVM PSRFPNLLVN GAAGIAVGMA TNIPPHQLGE IIDGVLAVSE
210 220 230 240 250
NPDITIPELM EVIPGPDFPT AGQILGRSGI RKAYESGRGS ITIRAKAEIE
260 270 280 290 300
QTSSGKERII VTELPYQVNK AKLIEKIADL VRDKKIEGIT DLRDESDRTG
310 320 330 340 350
MRIVIEIRRD ANANVILNNL YKQTALQTSF GINLLALVDG QPKVLTLKQC
360 370 380 390 400
LEHYLDHQKV VIRRRTAYEL RKAEARAHIL EGLRVALDHL DAVISLIRNS
410 420 430 440 450
QTAEIARTGL IEQFSLTEKQ AQAILDMRLQ RLTGLEREKI EEEYQSLVKL
460 470 480 490 500
IAELKDILAN EYKVLEIIRE ELTEIKERFN DERRTEIVTS GLETIEDEDL
510 520 530 540 550
IERENIVVTL THNGYVKRLP ASTYRSQKRG GKGVQGMGTN EDDFVEHLIS
560 570 580 590 600
TSTHDTILFF SNKGKVYRAK GYEIPEYGRT AKGIPIINLL EVEKGEWINA
610 620 630 640 650
IIPVTEFNAE LYLFFTTKHG VSKRTSLSQF ANIRNNGLIA LSLREDDELM
660 670 680 690 700
GVRLTDGTKQ IIIGTKNGLL IRFPETDVRE MGRTAAGVKG ITLTDDDVVV
710 720 730 740 750
GMEILEEESH VLIVTEKGYG KRTPAEEYRT QSRGGKGLKT AKITENNGQL
760 770 780 790 800
VAVKATKGEE DLMIITASGV LIRMDINDIS ITGRVTQGVR LIRMAEEEHV
810 820
ATVALVEKNE EDENEEEQEE V
Length:821
Mass (Da):92,099
Last modified:November 1, 1988 - v1
Checksum:i717847A5F35FB857
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02369 Genomic DNA. Translation: CAA26222.1.
D26185 Genomic DNA. Translation: BAA05243.1.
AL009126 Genomic DNA. Translation: CAB11783.1.
PIRiF22930.
RefSeqiNP_387888.1. NC_000964.3.

Genome annotation databases

EnsemblBacteriaiCAB11783; CAB11783; BSU00070.
GeneIDi940002.
KEGGibsu:BSU00070.
PATRICi18971463. VBIBacSub10457_0008.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02369 Genomic DNA. Translation: CAA26222.1 .
D26185 Genomic DNA. Translation: BAA05243.1 .
AL009126 Genomic DNA. Translation: CAB11783.1 .
PIRi F22930.
RefSeqi NP_387888.1. NC_000964.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4DDQ X-ray 3.30 A/B/C/D/E/F 1-502 [» ]
ProteinModelPortali P05653.
SMRi P05653. Positions 11-809.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi P05653. 5 interactions.
MINTi MINT-8366974.
STRINGi 224308.BSU00070.

Chemistry

BindingDBi P05653.

Proteomic databases

PaxDbi P05653.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai CAB11783 ; CAB11783 ; BSU00070 .
GeneIDi 940002.
KEGGi bsu:BSU00070.
PATRICi 18971463. VBIBacSub10457_0008.

Organism-specific databases

GenoListi BSU00070. [Micado ]

Phylogenomic databases

eggNOGi COG0188.
HOGENOMi HOG000076278.
InParanoidi P05653.
KOi K02469.
OMAi QTVFGIN.
OrthoDBi EOG661H5V.
PhylomeDBi P05653.

Enzyme and pathway databases

BioCyci BSUB:BSU00070-MONOMER.

Miscellaneous databases

PROi P05653.

Family and domain databases

Gene3Di 3.30.1360.40. 1 hit.
3.90.199.10. 2 hits.
HAMAPi MF_01897. GyrA.
InterProi 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 ]
Pfami PF03989. DNA_gyraseA_C. 6 hits.
PF00521. DNA_topoisoIV. 1 hit.
[Graphical view ]
SMARTi SM00434. TOP4c. 1 hit.
[Graphical view ]
SUPFAMi SSF56719. SSF56719. 1 hit.
TIGRFAMsi TIGR01063. gyrA. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.

Entry informationi

Entry nameiGYRA_BACSU
AccessioniPrimary (citable) accession number: P05653
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: November 1, 1988
Last modified: November 26, 2014
This is version 113 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3