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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Streptococcus pneumoniae
Status
Unreviewed-Annotation score: -Experimental evidence at protein leveli

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

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

Catalytic activityi

ATP-dependent breakage, passage and rejoining of double-stranded DNA.UniRule annotationSAAS annotation

Cofactori

Protein has several cofactor binding sites:
  • Mg2+SAAS annotation
  • Mn2+SAAS annotation

Keywordsi

Molecular functionDNA-bindingSAAS annotation, Isomerase, TopoisomeraseUniRule annotationSAAS annotation
LigandATP-bindingUniRule annotationSAAS annotation, MagnesiumSAAS annotation, Metal-bindingSAAS annotation, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit BUniRule annotation (EC:5.99.1.3UniRule annotation)
Gene namesi
Name:gyrBUniRule annotationImported
Synonyms:gyrB_1Imported, gyrB_2Imported, gyrB_3Imported
ORF Names:A5N45_07160Imported, ERS019416_01766Imported, ERS019595_01309Imported, ERS020491_02088Imported, ERS021057_00935Imported, ERS021300_00002Imported, ERS021368_02050Imported, ERS021447_06941Imported, ERS021634_06258Imported, ERS022045_05472Imported, ERS022199_01981Imported, ERS022232_05511Imported, ERS050646_01103Imported, ERS232471_00791Imported, ERS232499_02012Imported, KK0981_27750Imported, SAMEA1026438_02006Imported, SAMEA2626854_02053Imported
OrganismiStreptococcus pneumoniaeImported
Taxonomic identifieri1313 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
Proteomesi
  • UP000046356 Componenti: Unassembled WGS sequence
  • UP000046081 Componenti: Unassembled WGS sequence
  • UP000046964 Componenti: Unassembled WGS sequence
  • UP000070772 Componenti: Unassembled WGS sequence
  • UP000045409 Componenti: Unassembled WGS sequence
  • UP000047188 Componenti: Unassembled WGS sequence
  • UP000041568 Componenti: Unassembled WGS sequence
  • UP000044228 Componenti: Unassembled WGS sequence
  • UP000197833 Componenti: Unassembled WGS sequence
  • UP000039362 Componenti: Unassembled WGS sequence
  • UP000043857 Componenti: Unassembled WGS sequence
  • UP000043492 Componenti: Unassembled WGS sequence
  • UP000218786 Componenti: Chromosome
  • UP000048265 Componenti: Unassembled WGS sequence
  • UP000214939 Componenti: Unassembled WGS sequence
  • UP000222964 Componenti: Unassembled WGS sequence
  • UP000043644 Componenti: Unassembled WGS sequence
  • UP000044638 Componenti: Unassembled WGS sequence

Subcellular locationi

  • Cytoplasm UniRule 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

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4Z2CX-ray3.19C/D404-648[»]
4Z2DX-ray3.38C/D404-648[»]
4Z2EX-ray3.46C/D404-648[»]
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini427 – 541ToprimInterPro annotationAdd BLAST115

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili302 – 322Sequence analysisAdd BLAST21

Sequence similaritiesi

Belongs to the type II topoisomerase family.UniRule annotation

Keywords - Domaini

Coiled coilSequence analysis

Phylogenomic databases

eggNOGiENOG4105C7D Bacteria
COG0187 LUCA

Family and domain databases

CDDicd00075 HATPase_c, 1 hit
cd03366 TOPRIM_TopoIIA_GyrB, 1 hit
Gene3Di3.30.230.10, 1 hit
3.30.565.10, 1 hit
3.40.50.670, 1 hit
HAMAPiMF_01898 GyrB, 1 hit
InterProiView protein in InterPro
IPR002288 DNA_gyrase_B_C
IPR011557 GyrB
IPR003594 HATPase_C
IPR036890 HATPase_C_sf
IPR020568 Ribosomal_S5_D2-typ_fold
IPR014721 Ribosomal_S5_D2-typ_fold_subgr
IPR001241 Topo_IIA
IPR013760 Topo_IIA-like_dom_sf
IPR013759 Topo_IIA_B_C
IPR013506 Topo_IIA_bsu_dom2
IPR018522 TopoIIA_CS
IPR006171 TOPRIM_domain
IPR034160 TOPRIM_GyrB
PANTHERiPTHR10169 PTHR10169, 1 hit
PfamiView protein in Pfam
PF00204 DNA_gyraseB, 1 hit
PF00986 DNA_gyraseB_C, 1 hit
PF02518 HATPase_c, 1 hit
PF01751 Toprim, 1 hit
SMARTiView protein in SMART
SM00387 HATPase_c, 1 hit
SM00433 TOP2c, 1 hit
SUPFAMiSSF54211 SSF54211, 1 hit
SSF55874 SSF55874, 1 hit
SSF56719 SSF56719, 1 hit
TIGRFAMsiTIGR01059 gyrB, 1 hit
PROSITEiView protein in PROSITE
PS00177 TOPOISOMERASE_II, 1 hit
PS50880 TOPRIM, 1 hit

Sequencei

Sequence statusi: Complete.

Q59957-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTEEIKNLQA QDYDASQIQV LEGLEAVRMR PGMYIGSTSK EGLHHLVWEI
60 70 80 90 100
VDNSIDEALA GFASHIQVFI EPDDSITVVD DGRGIPVDIQ EKTGRPAVET
110 120 130 140 150
VFTVLHAGGK FGGGGYKVSG GLHGVGSSVV NALSTQLDVH VHKNGKIHYQ
160 170 180 190 200
EYRRGHVVAD LEVVGDTDRT GTTVHFTPDP EIFTETTIFD FDKLNKRIQE
210 220 230 240 250
LAFLNRGLQI SITDKRQGLE QTKHYHYEGG IASYVEYINE NKDVIFDTPI
260 270 280 290 300
YTDGEMDDIT VEVAMQYTTG YHENVMSFAN NIHTHEGGTH EQGFRTALTR
310 320 330 340 350
VINDYARKNK LLKDNEDNLT GEDVREGLTA VISVKHPNPQ FEGQTKTKLG
360 370 380 390 400
NSEVVKITNR LFSEAFSDFL MENPQIAKRI VEKGILAAKA RVAAKRAREV
410 420 430 440 450
TRKKSGLEIS NLPGKLADCS SNNPAETELF IVEGDSAGGS AKSGRNREFQ
460 470 480 490 500
AILPIRGKIL NVEKASMDKI LANEEIRSLF TAMGTGFGAE FDVSKARYQK
510 520 530 540 550
LVLMTDADVD GAHIRTLLLT LIYRYMKPIL EAGYVYIAQP PIYGVKVGSE
560 570 580 590 600
IKEYIQPGAD QEIKLQEALA RYSEGRTKPT IQRYKGLGEM DDHQLWETTM
610 620 630 640
DPEHRLMARV SVDDAAEADK IFDMLMGDRV EPRREFIEEN AVYSTLDV
Length:648
Mass (Da):72,252
Last modified:November 1, 1996 - v1
Checksum:i65DB9BA2948933F6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
DQ175189 Genomic DNA Translation: AAZ92990.1
DQ175198 Genomic DNA Translation: AAZ92999.1
DQ175205 Genomic DNA Translation: AAZ93006.1
DQ175211 Genomic DNA Translation: AAZ93012.1
DQ175216 Genomic DNA Translation: AAZ93017.1
DQ175217 Genomic DNA Translation: AAZ93018.1
DQ175218 Genomic DNA Translation: AAZ93019.1
DQ175219 Genomic DNA Translation: AAZ93020.1
DQ175220 Genomic DNA Translation: AAZ93021.1
DQ175221 Genomic DNA Translation: AAZ93022.1
DQ175222 Genomic DNA Translation: AAZ93023.1
DQ175223 Genomic DNA Translation: AAZ93024.1
DQ175224 Genomic DNA Translation: AAZ93025.1
DQ175225 Genomic DNA Translation: AAZ93026.1
DQ175227 Genomic DNA Translation: AAZ93028.1
DQ175230 Genomic DNA Translation: AAZ93031.1
DQ175232 Genomic DNA Translation: AAZ93033.1
DQ175233 Genomic DNA Translation: AAZ93034.1
DQ175234 Genomic DNA Translation: AAZ93035.1
DQ175236 Genomic DNA Translation: AAZ93037.1
DQ175237 Genomic DNA Translation: AAZ93038.1
DQ175238 Genomic DNA Translation: AAZ93039.1
DQ175242 Genomic DNA Translation: AAZ93043.1
AP017971 Genomic DNA Translation: BAW84271.1
Z67740 Genomic DNA Translation: CAA91553.1
CFBA01000009 Genomic DNA Translation: CEV47067.1
CFGX01000042 Genomic DNA Translation: CEY69335.1
CHOW01000038 Genomic DNA Translation: CGF84100.1
CKJB01000009 Genomic DNA Translation: CIT95303.1
CKOI01000026 Genomic DNA Translation: CIX15593.1
CKVN01000072 Genomic DNA Translation: CJD01833.1
CLBL01000001 Genomic DNA Translation: CJF15045.1
CLFU01000080 Genomic DNA Translation: CJJ98829.1
CLJU01000083 Genomic DNA Translation: CJM24679.1
CLMB01000057 Genomic DNA Translation: CJM85438.1
CLNH01000027 Genomic DNA Translation: CJO19086.1
CMOR01000008 Genomic DNA Translation: CKE01452.1
CMQD01000051 Genomic DNA Translation: CKF18426.1
FIYI01000011 Genomic DNA Translation: CZD98934.1
NNBW01000096 Genomic DNA Translation: OYL27933.1
FYHW01000038 Genomic DNA Translation: SNE64228.1
FZDQ01000025 Genomic DNA Translation: SNP80995.1
RefSeqiWP_000134047.1, NZ_PIZF01000018.1

Genome annotation databases

PATRICifig|1313.5281.peg.1921

Similar proteinsi

Entry informationi

Entry nameiQ59957_STREE
AccessioniPrimary (citable) accession number: Q59957
Entry historyiIntegrated into UniProtKB/TrEMBL: November 1, 1996
Last sequence update: November 1, 1996
Last modified: April 25, 2018
This is version 146 of the entry and version 1 of the sequence. See complete history.
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteomeImported
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Main funding by: National Institutes of Health