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Q1RHT8

- GYRB_RICBR

UniProt

Q1RHT8 - GYRB_RICBR

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Protein

DNA gyrase subunit B

Gene
gyrB, RBE_0995
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 By similarity.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+ By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi435 – 4351Magnesium 1; catalytic By similarity
Sitei460 – 4601Interaction with DNA By similarity
Sitei463 – 4631Interaction with DNA By similarity
Metal bindingi509 – 5091Magnesium 1; catalytic By similarity
Metal bindingi509 – 5091Magnesium 2 By similarity
Metal bindingi511 – 5111Magnesium 2 By similarity

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 B (EC:5.99.1.3)
Gene namesi
Name:gyrB
Ordered Locus Names:RBE_0995
OrganismiRickettsia bellii (strain RML369-C)
Taxonomic identifieri336407 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRickettsialesRickettsiaceaeRickettsieaeRickettsiabelli group
ProteomesiUP000001951: Chromosome

Subcellular locationi

Cytoplasm Reviewed prediction UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 808808DNA gyrase subunit BUniRule annotationPRO_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 By similarity.

Protein-protein interaction databases

STRINGi336407.RBE_0995.

Structurei

3D structure databases

ProteinModelPortaliQ1RHT8.

Family & Domainsi

Domains and Repeats

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

Sequence similaritiesi

Contains 1 Toprim domain.

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_ATP-bd.
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

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MSEFEEKLNE SSYGADSIKV LKGLEAVRKR PGMYIGDVGD GSGLHHMIYE    50
VVDNAIDEAL AGYCDLVRVV LNKNGSVTVS DNGRGIPVEI HEEEGISAAE 100
VIMTQLHAGG KFDQNSYKVS GGLHGVGVSV VNALSDWLEL RIWRNNTEHL 150
IRFNNGITEA PLAVVKENVD KKGTEVTFFP SVETFTNIEF DFSIIEHRLR 200
ELAFLNSGVK ILLTDNRFEE VKEVEFYYTG GIEAYVKYLD RAKHAVHSCI 250
VVNADNTESG ISLELAMHWN DSYHENILCF TNNIRQRDGG THLSAFKSGL 300
TRVITAYLEN TGLNKKAKNA FSGEDTREGI CCVLSVKVPD PKFSSQTKDK 350
LVSSEVRPIV ENAVYTKVLE WFEEHPADAK LIINKIMEAA NAREAARKAR 400
ELTRRKSVLE VSNLPGKLAD CHAKDPAVSE LFIVEGDSAG GTAKQGRDSK 450
IQAILPLRGK ILNVERARFD KMLGSDQIGT LITALGTGVD NREFSLEKLR 500
YHKVIIMTDA DVDGSHIRTL LLTFFYRHMP ELINKGYLYI AQPPLYKVKK 550
GASELYLKNE QALQDYLVKS AISDATLTLD NKEQLTNENL EELMSKVIKF 600
NSLLDHASKK FNRSITEILA INDLLNNKIF DNESDSRLKK ALNALNSLEQ 650
SPDKTDWEVL KHENKIEFFR FSRGLKERKI LLREQLESFE FINISKLALT 700
IFDVFNKQLK LVVKNQEFDI LTPSILLNTI IECGKKGISV QRFKGLGEMN 750
SDQLWDTTLD PKKRTLMQVR VAEVDEAEGI FSTLMGDVVE PRRQFIQSNA 800
LNVVNLDV 808
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.
RefSeqiYP_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 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_ATP-bd.
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: May 14, 2014
This is version 57 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

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