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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Rickettsia bellii (strain RML369-C)
Status
Reviewed-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 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 bindingi435 – 4351Magnesium 1; catalyticUniRule annotation
Sitei460 – 4601Interaction with DNAUniRule annotation
Sitei463 – 4631Interaction with DNAUniRule annotation
Metal bindingi509 – 5091Magnesium 1; catalyticUniRule annotation
Metal bindingi509 – 5091Magnesium 2UniRule annotation
Metal bindingi511 – 5111Magnesium 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

BioCyciRBEL336407:GJCY-1022-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit BUniRule annotation (EC:5.99.1.3UniRule annotation)
Gene namesi
Name:gyrBUniRule annotation
Ordered Locus Names:RBE_0995
OrganismiRickettsia bellii (strain RML369-C)
Taxonomic identifieri336407 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRickettsialesRickettsiaceaeRickettsieaeRickettsiabelli group
ProteomesiUP000001951 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 – 808808DNA gyrase subunit BPRO_0000273110Add
BLAST

Proteomic databases

PRIDEiQ1RHT8.

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

Structurei

3D structure databases

ProteinModelPortaliQ1RHT8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini429 – 544116ToprimUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0187.
HOGENOMiHOG000075155.
KOiK02470.
OMAiIFETTEF.
OrthoDBiEOG6P334W.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 2 hits.
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. 2 hits.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q1RHT8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEFEEKLNE SSYGADSIKV LKGLEAVRKR PGMYIGDVGD GSGLHHMIYE
60 70 80 90 100
VVDNAIDEAL AGYCDLVRVV LNKNGSVTVS DNGRGIPVEI HEEEGISAAE
110 120 130 140 150
VIMTQLHAGG KFDQNSYKVS GGLHGVGVSV VNALSDWLEL RIWRNNTEHL
160 170 180 190 200
IRFNNGITEA PLAVVKENVD KKGTEVTFFP SVETFTNIEF DFSIIEHRLR
210 220 230 240 250
ELAFLNSGVK ILLTDNRFEE VKEVEFYYTG GIEAYVKYLD RAKHAVHSCI
260 270 280 290 300
VVNADNTESG ISLELAMHWN DSYHENILCF TNNIRQRDGG THLSAFKSGL
310 320 330 340 350
TRVITAYLEN TGLNKKAKNA FSGEDTREGI CCVLSVKVPD PKFSSQTKDK
360 370 380 390 400
LVSSEVRPIV ENAVYTKVLE WFEEHPADAK LIINKIMEAA NAREAARKAR
410 420 430 440 450
ELTRRKSVLE VSNLPGKLAD CHAKDPAVSE LFIVEGDSAG GTAKQGRDSK
460 470 480 490 500
IQAILPLRGK ILNVERARFD KMLGSDQIGT LITALGTGVD NREFSLEKLR
510 520 530 540 550
YHKVIIMTDA DVDGSHIRTL LLTFFYRHMP ELINKGYLYI AQPPLYKVKK
560 570 580 590 600
GASELYLKNE QALQDYLVKS AISDATLTLD NKEQLTNENL EELMSKVIKF
610 620 630 640 650
NSLLDHASKK FNRSITEILA INDLLNNKIF DNESDSRLKK ALNALNSLEQ
660 670 680 690 700
SPDKTDWEVL KHENKIEFFR FSRGLKERKI LLREQLESFE FINISKLALT
710 720 730 740 750
IFDVFNKQLK LVVKNQEFDI LTPSILLNTI IECGKKGISV QRFKGLGEMN
760 770 780 790 800
SDQLWDTTLD PKKRTLMQVR VAEVDEAEGI FSTLMGDVVE PRRQFIQSNA

LNVVNLDV
Length:808
Mass (Da):90,843
Last modified:May 16, 2006 - v1
Checksum:i9A6B883F87D5D26F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000087 Genomic DNA. Translation: ABE05076.1.
RefSeqiWP_011477656.1. NC_007940.1.
YP_538165.1. NC_007940.1.

Genome annotation databases

EnsemblBacteriaiABE05076; ABE05076; RBE_0995.
KEGGirbe:RBE_0995.
PATRICi17883537. VBIRicBel102610_1127.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000087 Genomic DNA. Translation: ABE05076.1.
RefSeqiWP_011477656.1. NC_007940.1.
YP_538165.1. NC_007940.1.

3D structure databases

ProteinModelPortaliQ1RHT8.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiQ1RHT8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABE05076; ABE05076; RBE_0995.
KEGGirbe:RBE_0995.
PATRICi17883537. VBIRicBel102610_1127.

Phylogenomic databases

eggNOGiCOG0187.
HOGENOMiHOG000075155.
KOiK02470.
OMAiIFETTEF.
OrthoDBiEOG6P334W.

Enzyme and pathway databases

BioCyciRBEL336407:GJCY-1022-MONOMER.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 2 hits.
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. 2 hits.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens."
    Ogata H., La Scola B., Audic S., Renesto P., Blanc G., Robert C., Fournier P.-E., Claverie J.-M., Raoult D.
    PLoS Genet. 2:733-744(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: RML369-C.

Entry informationi

Entry nameiGYRB_RICBR
AccessioniPrimary (citable) accession number: Q1RHT8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 23, 2007
Last sequence update: May 16, 2006
Last modified: June 24, 2015
This is version 66 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

Complete proteome

Documents

  1. Rickettsia bellii strain RML369-C
    Rickettsia bellii (strain RML369-C): entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families

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.