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Q1RHT8

- GYRB_RICBR

UniProt

Q1RHT8 - GYRB_RICBR

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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Rickettsia bellii (strain RML369-C)
Status
Reviewed - 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

Magnesium. 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+ and 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

  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, 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: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. chromosome Source: InterPro
  2. cytoplasm Source: UniProtKB-HAMAP
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

Protein-protein interaction databases

STRINGi336407.RBE_0995.

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.
OMAiHIIIMTD.
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:
EMBL
GenBank
DDBJ
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.
GeneIDi3994964.
KEGGirbe:RBE_0995.
PATRICi17883537. VBIRicBel102610_1127.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP000087 Genomic DNA. Translation: ABE05076.1 .
RefSeqi WP_011477656.1. NC_007940.1.
YP_538165.1. NC_007940.1.

3D structure databases

ProteinModelPortali Q1RHT8.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 336407.RBE_0995.

Proteomic databases

PRIDEi Q1RHT8.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ABE05076 ; ABE05076 ; RBE_0995 .
GeneIDi 3994964.
KEGGi rbe:RBE_0995.
PATRICi 17883537. VBIRicBel102610_1127.

Phylogenomic databases

eggNOGi COG0187.
HOGENOMi HOG000075155.
KOi K02470.
OMAi HIIIMTD.
OrthoDBi EOG6P334W.

Enzyme and pathway databases

BioCyci RBEL336407:GJCY-1022-MONOMER.

Family and domain databases

Gene3Di 3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 2 hits.
HAMAPi MF_01898. GyrB.
InterProi IPR002288. 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 ]
Pfami PF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view ]
PRINTSi PR00418. TPI2FAMILY.
SMARTi SM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view ]
SUPFAMi SSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 2 hits.
TIGRFAMsi TIGR01059. gyrB. 1 hit.
PROSITEi PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view ]
ProtoNeti Search...

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: October 29, 2014
This is version 59 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