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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Syntrophothermus lipocalidus (strain DSM 12680 / TGB-C1)
Status
Unreviewed-Annotation score: Annotation score: 3 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 annotationSAAS 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, TopoisomeraseUniRule annotationSAAS annotation

Keywords - Ligandi

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

Enzyme and pathway databases

BioCyciSLIP643648:GHUR-5-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit BUniRule annotationSAAS annotation (EC:5.99.1.3UniRule annotationSAAS annotation)
Gene namesi
Name:gyrBUniRule annotation
Ordered Locus Names:Slip_0005Imported
OrganismiSyntrophothermus lipocalidus (strain DSM 12680 / TGB-C1)Imported
Taxonomic identifieri643648 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesSyntrophomonadaceaeSyntrophothermus
Proteomesi
  • UP000000378 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotation

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

STRINGi643648.Slip_0005.

Structurei

3D structure databases

ProteinModelPortaliD7CPP1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini421 – 535115ToprimInterPro annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
HOGENOMiHOG000075154.
KOiK02470.
OMAiIKNMITA.

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.

D7CPP1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNINGSKNEY TALDIQVLEG LEAVRKRPGM YIGSTDSRGL HHLVFEIVDN
60 70 80 90 100
SIDEAVAGYC DEIKVIILDD STVTVTDNGR GIPVDMHPKM GIPALEVILT
110 120 130 140 150
TLHSGAKFGG SGYTISGGLH GVGLSVVNAL SRWLEVEVAR DGQLYHQRYE
160 170 180 190 200
RGKPVTPLAV TGACQTTGTK ITFSPDPEIF EEICFSAEII GQRLRELSYL
210 220 230 240 250
NQGTRIVLCD KRTGRDVEYY HTGGIRDFVK YLSKNREPLS PEPIYFRIGK
260 270 280 290 300
EGTVVEVAIQ YNTGYTETLL SYANNIHTQE GGTHELGFKN GLTRVVNEYA
310 320 330 340 350
KKQGMLKENE GNLLGEDIRE GMTAVISVLV QDPQFEGQTK TKLGNAFIRS
360 370 380 390 400
LVEGAVSDFV GAFFDENPSL AKKIVEKAIA ARRAREAARK ARELTRRKNL
410 420 430 440 450
LDSTSLPGKL ADCSEKDPAL SELYLVEGDS AGGSAKQGRD RNFQAILPLR
460 470 480 490 500
GKILNVEKAR LDKVLSNEEI RALITAIGTG IGEDFDINKA RYHRLIIMTD
510 520 530 540 550
ADVDGSHIRV LLLTFFYRYM RPLIEAGYVY VAQPPLYELK RGKEVHYIYN
560 570 580 590 600
DRELQRFLEQ QGNKKYGVKR YKGLGEMNPE QLWETTMNPE NRTLLQVRIE
610 620 630
DAIAADVIFS SLMGEKVEPR REFIQENARL VTNLDI
Length:636
Mass (Da):71,076
Last modified:August 10, 2010 - v1
Checksum:i0799A7E8050557BF
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002048 Genomic DNA. Translation: ADI00813.1.
RefSeqiWP_013174217.1. NC_014220.1.

Genome annotation databases

EnsemblBacteriaiADI00813; ADI00813; Slip_0005.
KEGGislp:Slip_0005.
PATRICi38266332. VBISynLip21176_0006.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002048 Genomic DNA. Translation: ADI00813.1.
RefSeqiWP_013174217.1. NC_014220.1.

3D structure databases

ProteinModelPortaliD7CPP1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi643648.Slip_0005.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADI00813; ADI00813; Slip_0005.
KEGGislp:Slip_0005.
PATRICi38266332. VBISynLip21176_0006.

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
HOGENOMiHOG000075154.
KOiK02470.
OMAiIKNMITA.

Enzyme and pathway databases

BioCyciSLIP643648:GHUR-5-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.
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

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 12680 / TGB-C1Imported.

Entry informationi

Entry nameiD7CPP1_SYNLT
AccessioniPrimary (citable) accession number: D7CPP1
Entry historyi
Integrated into UniProtKB/TrEMBL: August 10, 2010
Last sequence update: August 10, 2010
Last modified: March 16, 2016
This is version 50 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

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 proteomeImported

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.