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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
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 bindingi427 – 4271Magnesium 1; catalyticUniRule annotation
Metal bindingi500 – 5001Magnesium 1; catalyticUniRule annotation
Metal bindingi500 – 5001Magnesium 2UniRule annotation
Metal bindingi502 – 5021Magnesium 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

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit BUniRule annotation (EC:5.99.1.3UniRule annotation)
Gene namesi
Name:gyrBUniRule annotation
Synonyms:top2B
Ordered Locus Names:TM_0833
OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Taxonomic identifieri243274 [NCBI]
Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
Proteomesi
  • UP000008183 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 – 636636DNA gyrase subunit BPRO_0000145355Add
BLAST

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
Sitei452 – 4521Interaction with DNAUniRule annotation
Sitei455 – 4551Interaction with DNAUniRule annotation

Protein-protein interaction databases

STRINGi243274.TM0833.

Structurei

3D structure databases

ProteinModelPortaliP77993.
SMRiP77993. Positions 8-395.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini421 – 535115ToprimUniRule 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.
InParanoidiP77993.
KOiK02470.
OMAiIKNMITA.
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.
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.

P77993-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEKYSAESIK VLKGLEPVRM RPGMYIGSTG KRGLHHLVYE VVDNSVDEAL
60 70 80 90 100
AGYCDWIRVT LHEDGSVEVE DNGRGIPVDI HPEEGRSALE VVFTVLHAGG
110 120 130 140 150
KFSKDSYKIS GGLHGVGVSV VNALSEWLEV RVHRDGKIYR QRYERGKPVT
160 170 180 190 200
PVEVIGETDK HGTIVRFKPD PLIFSETEFD PDILEHRLRE IAFLVPGLKI
210 220 230 240 250
EFEDRINGEK KTFKFDGGIV EYVKYLNRGK KALHDVIHIK RTEKVKTKNG
260 270 280 290 300
EDEVIVEIAF QYTDSYSEDI VSFANTIKTV DGGTHVTAFK STLTRLMNEY
310 320 330 340 350
GKKHNFLKKD DSFQGEDVRE GLTAVISVYV KNPEFEGQTK SKLGNEEVKE
360 370 380 390 400
AVTKAMREEL KKIFDANPEL VKTILSKIMS TKQAREAAKR AREMVRRKNV
410 420 430 440 450
LQNTTLPGKL ADCSSTHREK TELFIVEGDS AGGSAKQARD REFQAVLPIR
460 470 480 490 500
GKILNVEKSS LDRLLKNEQI SDIIVAVGTG IGDDFDESKL RYGRIIIMTD
510 520 530 540 550
ADIDGAHIRT LLLTLFYRYM RPLIEQGRVY IALPPLYRIK AGREEFYVYS
560 570 580 590 600
DQELAEYKEK LQGKRIEIQR YKGLGEMNPE QLWETTMNPE TRKIIRVTIE
610 620 630
DAEEADRLFE ILMGNDPSSR REFIERHALK VKELDI
Length:636
Mass (Da):72,428
Last modified:May 30, 2000 - v2
Checksum:iB21E0E0CBEC6F89E
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti152 – 1521V → M in AAC44498 (PubMed:8863738).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U49692 Genomic DNA. Translation: AAC44498.1.
AE000512 Genomic DNA. Translation: AAD35915.1.
PIRiJC4960.
RefSeqiNP_228642.1. NC_000853.1.
WP_004080806.1. NZ_CP011107.1.

Genome annotation databases

EnsemblBacteriaiAAD35915; AAD35915; TM_0833.
GeneIDi898504.
KEGGitma:TM0833.
PATRICi23936592. VBITheMar51294_0846.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U49692 Genomic DNA. Translation: AAC44498.1.
AE000512 Genomic DNA. Translation: AAD35915.1.
PIRiJC4960.
RefSeqiNP_228642.1. NC_000853.1.
WP_004080806.1. NZ_CP011107.1.

3D structure databases

ProteinModelPortaliP77993.
SMRiP77993. Positions 8-395.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243274.TM0833.

Protocols and materials databases

DNASUi898504.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD35915; AAD35915; TM_0833.
GeneIDi898504.
KEGGitma:TM0833.
PATRICi23936592. VBITheMar51294_0846.

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
InParanoidiP77993.
KOiK02470.
OMAiIKNMITA.
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.
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. "A gyrB-like gene from the hyperthermophilic bacterion Thermotoga maritima."
    Guipaud O., Labedan B., Forterre P.
    Gene 174:121-128(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.

Entry informationi

Entry nameiGYRB_THEMA
AccessioniPrimary (citable) accession number: P77993
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 30, 2000
Last modified: June 8, 2016
This is version 129 of the entry and version 2 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. 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.