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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner.UniRule annotation

Catalytic activityi

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

Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotation, Ca2+UniRule annotationNote: Binds two Mg2+ per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn2+ or Ca2+.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi428 – 4281Magnesium 1; catalyticUniRule annotation
Metal bindingi501 – 5011Magnesium 1; catalyticUniRule annotation
Metal bindingi501 – 5011Magnesium 2UniRule annotation
Metal bindingi503 – 5031Magnesium 2UniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciBSUB:BSU00060-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit BUniRule annotation (EC:5.99.1.3UniRule annotation)
Gene namesi
Name:gyrBUniRule annotation
Synonyms:novA
Ordered Locus Names:BSU00060
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 638638DNA gyrase subunit BPRO_0000145294Add
BLAST

Proteomic databases

PaxDbiP05652.
PRIDEiP05652.

Interactioni

Subunit structurei

Heterotetramer, composed of two GyrA and two GyrB chains. In the heterotetramer, GyrA contains the active site tyrosine that forms a transient covalent intermediate with DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei453 – 4531Interaction with DNAUniRule annotation
Sitei456 – 4561Interaction with DNAUniRule annotation

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100000030.

Chemistry

BindingDBiP05652.

Structurei

3D structure databases

ProteinModelPortaliP05652.
SMRiP05652. Positions 6-395, 409-637.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini422 – 536115ToprimUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the type II topoisomerase GyrB family.UniRule annotation
Contains 1 Toprim domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
HOGENOMiHOG000075156.
InParanoidiP05652.
KOiK02470.
OMAiIKNMITA.
OrthoDBiEOG6P334W.
PhylomeDBiP05652.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPiMF_01898. GyrB.
InterProiIPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_C.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR013760. Topo_IIA-like_dom.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]
PfamiPF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00418. TPI2FAMILY.
SMARTiSM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P05652-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEQQQNSYDE NQIQVLEGLE AVRKRPGMYI GSTNSKGLHH LVWEIVDNSI
60 70 80 90 100
DEALAGYCTD INIQIEKDNS ITVVDNGRGI PVGIHEKMGR PAVEVIMTVL
110 120 130 140 150
HAGGKFDGSG YKVSGGLHGV GASVVNALST ELDVTVHRDG KIHRQTYKRG
160 170 180 190 200
VPVTDLEIIG ETDHTGTTTH FVPDPEIFSE TTEYDYDLLA NRVRELAFLT
210 220 230 240 250
KGVNITIEDK REGQERKNEY HYEGGIKSYV EYLNRSKEVV HEEPIYIEGE
260 270 280 290 300
KDGITVEVAL QYNDSYTSNI YSFTNNINTY EGGTHEAGFK TGLTRVINDY
310 320 330 340 350
ARKKGLIKEN DPNLSGDDVR EGLTAIISIK HPDPQFEGQT KTKLGNSEAR
360 370 380 390 400
TITDTLFSTA METFMLENPD AAKKIVDKGL MAARARMAAK KARELTRRKS
410 420 430 440 450
ALEISNLPGK LADCSSKDPS ISELYIVEGD SAGGSAKQGR DRHFQAILPL
460 470 480 490 500
RGKILNVEKA RLDKILSNNE VRSMITALGT GIGEDFNLEK ARYHKVVIMT
510 520 530 540 550
DADVDGAHIR TLLLTFFYRY MRQIIENGYV YIAQPPLYKV QQGKRVEYAY
560 570 580 590 600
NDKELEELLK TLPQTPKPGL QRYKGLGEMN ATQLWETTMD PSSRTLLQVT
610 620 630
LEDAMDADET FEMLMGDKVE PRRNFIEANA RYVKNLDI
Length:638
Mass (Da):71,504
Last modified:November 1, 1988 - v1
Checksum:iF84F9D3B084F6118
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02369 Genomic DNA. Translation: CAA26221.1.
D26185 Genomic DNA. Translation: BAA05242.1.
AL009126 Genomic DNA. Translation: CAB11782.1.
PIRiE22930.
RefSeqiNP_387887.1. NC_000964.3.
WP_003226808.1. NZ_JNCM01000034.1.

Genome annotation databases

EnsemblBacteriaiCAB11782; CAB11782; BSU00060.
GeneIDi939456.
KEGGibsu:BSU00060.
PATRICi18971459. VBIBacSub10457_0006.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X02369 Genomic DNA. Translation: CAA26221.1.
D26185 Genomic DNA. Translation: BAA05242.1.
AL009126 Genomic DNA. Translation: CAB11782.1.
PIRiE22930.
RefSeqiNP_387887.1. NC_000964.3.
WP_003226808.1. NZ_JNCM01000034.1.

3D structure databases

ProteinModelPortaliP05652.
SMRiP05652. Positions 6-395, 409-637.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100000030.

Chemistry

BindingDBiP05652.

Proteomic databases

PaxDbiP05652.
PRIDEiP05652.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB11782; CAB11782; BSU00060.
GeneIDi939456.
KEGGibsu:BSU00060.
PATRICi18971459. VBIBacSub10457_0006.

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
HOGENOMiHOG000075156.
InParanoidiP05652.
KOiK02470.
OMAiIKNMITA.
OrthoDBiEOG6P334W.
PhylomeDBiP05652.

Enzyme and pathway databases

BioCyciBSUB:BSU00060-MONOMER.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPiMF_01898. GyrB.
InterProiIPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_C.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR013760. Topo_IIA-like_dom.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]
PfamiPF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00418. TPI2FAMILY.
SMARTiSM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

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 nameiGYRB_BACSU
AccessioniPrimary (citable) accession number: P05652
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: November 1, 1988
Last modified: June 8, 2016
This is version 133 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Few gyrases are as efficient as E.coli at forming negative supercoils. Not all organisms have 2 type II topoisomerases; in organisms with a single type II topoisomerase this enzyme also has to decatenate newly replicated chromosomes.UniRule annotation

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.