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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Nocardia farcinica (strain IFM 10152)
Status
Unreviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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 annotationSAAS annotation

Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotation, Ca2+UniRule annotationNote: Binds two Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) or Ca2+.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi480 – 4801Magnesium 1; catalyticUniRule annotation
Sitei505 – 5051Interaction with DNAUniRule annotation
Sitei508 – 5081Interaction with DNAUniRule annotation
Metal bindingi553 – 5531Magnesium 1; catalyticUniRule annotation
Metal bindingi553 – 5531Magnesium 2UniRule annotation
Metal bindingi555 – 5551Magnesium 2UniRule 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: UniProtKB-HAMAP
  4. magnesium ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. DNA-dependent DNA replication Source: UniProtKB-HAMAP
  2. DNA topological change Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, TopoisomeraseUniRule annotation

Keywords - Ligandi

ATP-bindingUniRule annotation, DNA-bindingUniRule annotation, MagnesiumUniRule annotation, Metal-bindingUniRule annotation, Nucleotide-binding

Enzyme and pathway databases

BioCyciNFAR247156:GJ9T-6-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit BUniRule annotation (EC:5.99.1.3UniRule annotation)
Gene namesi
Name:gyrBUniRule annotationImported
Ordered Locus Names:NFA_60Imported
OrganismiNocardia farcinica (strain IFM 10152)Imported
Taxonomic identifieri247156 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeNocardiaceaeNocardia
ProteomesiUP000006820 Componenti: Chromosome

Subcellular locationi

  1. Cytoplasm UniRule annotation

GO - Cellular componenti

  1. chromosome Source: InterPro
  2. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotation

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

STRINGi247156.nfa60.

Structurei

3D structure databases

ProteinModelPortaliQ5Z3Z3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini474 – 588115ToprimUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

KOiK02470.
OMAiIFETTEF.
OrthoDBiEOG6P334W.

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.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_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.

Q5Z3Z3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MCCAIATRRS ASKESYRPVA AKHSNESGSK STNYGASSIT VLEGLEAVRK
60 70 80 90 100
RPGMYIGSTG ERGLHHLIWE VVDNSVDEAM AGYATRVDVT LLADGGVEVV
110 120 130 140 150
DDGRGIPVEM HAQGIPTVEV VMTQLHAGGK FDSESYAVSG GLHGVGISVV
160 170 180 190 200
NALSSRVEVE IDVDGYHWSQ TYKEATPSKL VKGEPTDRTG TTVRFWADPE
210 220 230 240 250
IFETTTYNFE TVARRLQEMA FLNKGLTITL TDERVSESDV TDEIVSETAE
260 270 280 290 300
APKHGEPTGE AASEHKVKTR TYHYPGGLED FVRHINRTKQ AIHNSVVSFT
310 320 330 340 350
GKGTGHELEV AMQWNSGYSE SVHTFANTIN THEGGTHEEG FRAALTTVVN
360 370 380 390 400
KYAKDKKLLK EKDGNLTGDD IREGLAAIVS VKVAEPQFEG QTKTKLGNTE
410 420 430 440 450
VKSFVQRTCN EHLTHWFEAN PADAKTIVQK AVSSAQARVA ARKARELVRR
460 470 480 490 500
KSATDLGGLP GKLADCRSKD PSKSEIYIVE GDSAGGSAKS GRDSMYQAIL
510 520 530 540 550
PLRGKIINVE KARIDKVLKN NEVQSIITAF GTGIHDEFDI SKLRYHKIVL
560 570 580 590 600
MADADVDGQH ISTLLLTLLF RFMRPLVEHG HVYLAQPPLY KLKWQRSEPE
610 620 630 640 650
FAYSDRERDG LLERGLAAGK KINKDDGIQR YKGLGEMNPK ELWETTMDPS
660 670 680 690
VRVLRQVTLD DAAAADELFS VLMGEDVEAR RSFITRNAKD VRFLDV
Length:696
Mass (Da):76,678
Last modified:November 23, 2004 - v1
Checksum:i26B9306DC1221E59
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006618 Genomic DNA. Translation: BAD54848.1.
RefSeqiYP_116212.1. NC_006361.1.

Genome annotation databases

EnsemblBacteriaiBAD54848; BAD54848; NFA_60.
KEGGinfa:nfa60.
PATRICi22729460. VBINocFar94200_0006.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AP006618 Genomic DNA. Translation: BAD54848.1.
RefSeqiYP_116212.1. NC_006361.1.

3D structure databases

ProteinModelPortaliQ5Z3Z3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi247156.nfa60.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAD54848; BAD54848; NFA_60.
KEGGinfa:nfa60.
PATRICi22729460. VBINocFar94200_0006.

Phylogenomic databases

KOiK02470.
OMAiIFETTEF.
OrthoDBiEOG6P334W.

Enzyme and pathway databases

BioCyciNFAR247156:GJ9T-6-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.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_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

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: IFM 10152Imported.

Entry informationi

Entry nameiQ5Z3Z3_NOCFA
AccessioniPrimary (citable) accession number: Q5Z3Z3
Entry historyi
Integrated into UniProtKB/TrEMBL: November 23, 2004
Last sequence update: November 23, 2004
Last modified: April 29, 2015
This is version 94 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteomeImported

External Data

Dasty 3

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 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.