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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Status
Reviewed-Annotation score: -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

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 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)DescriptionActionsGraphical viewLength
Metal bindingi422Magnesium 1; catalyticUniRule annotation1
Metal bindingi495Magnesium 1; catalyticUniRule annotation1
Metal bindingi495Magnesium 2UniRule annotation1
Metal bindingi497Magnesium 2UniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Isomerase, Topoisomerase
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciHPY:HP0501-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:HP_0501
OrganismiHelicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Taxonomic identifieri85962 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
Proteomesi
  • UP000000429 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001453141 – 773DNA gyrase subunit BAdd BLAST773

Proteomic databases

PaxDbiP55992
PRIDEiP55992

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)DescriptionActionsGraphical viewLength
Sitei447Interaction with DNAUniRule annotation1
Sitei450Interaction with DNAUniRule annotation1

Protein-protein interaction databases

DIPiDIP-3593N
IntActiP55992, 3 interactors
MINTiP55992
STRINGi85962.HP0501

Structurei

3D structure databases

ProteinModelPortaliP55992
SMRiP55992
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini416 – 530ToprimUniRule annotationAdd BLAST115

Sequence similaritiesi

Belongs to the type II topoisomerase GyrB family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105C7D Bacteria
COG0187 LUCA
KOiK02470
OMAiDCSSRDP

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, 2 hits
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, 2 hits
TIGRFAMsiTIGR01059 gyrB, 1 hit
PROSITEiView protein in PROSITE
PS00177 TOPOISOMERASE_II, 1 hit
PS50880 TOPRIM, 1 hit

Sequencei

Sequence statusi: Complete.

P55992-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQNYQSHSIK VLKGLEGVRK RPGMYIGDTN VGGLHHMVYE VVDNAVDESM
60 70 80 90 100
AGFCDTINIT LTDEGSCIVE DNGRGIPVDI HPTEKIPACT VVLTILHAGG
110 120 130 140 150
KFDNDTYKVS GGLHGVGVSV VNALSKRLIM TIKKEGQIYR QEFEKGIPTS
160 170 180 190 200
ELEIIGKTKS AKESGTTIEF FPDESVMEVV EFQAGILQKR FKEMAYLNDG
210 220 230 240 250
LKISFKEEKT QLQETYFYED GLKQFVKDSA KKELLTPIIS FKSMDEETRT
260 270 280 290 300
SIEVALAYAD DYNENTLSFV NNIKTSEGGT HEAGFKMGLS KAILQYIGNN
310 320 330 340 350
IKTKESRPIS EDIKEGLIAV VSLKMSEPLF EGQTKSKLGS SYARALVSKL
360 370 380 390 400
VYDKIHQFLE ENPNEAKIIA NKALLAAKAR EASKKARELT RKKDNLSVGT
410 420 430 440 450
LPGKLADCQS KDPLESEIFL VEGDSAGGSA KQGRDRVFQA ILPLKGKILN
460 470 480 490 500
VEKSHLSKIL KSEEIKNMIT AFGCGIQESF DIERLRYHKI IIMTDADVDG
510 520 530 540 550
SHIQTLLMTF FYRYLRPLIE QGHVYIAQAP LYKYKKGKTE IYLKDSVALD
560 570 580 590 600
HFLIEHGINS VDIEGIGKND LMNLLKVARH YRYALLELEK RYNLLEILRF
610 620 630 640 650
LIETKDALSL DMKVLEKSIL EKLEGLNYQI LRSFATEESL HLHTQTPKGL
660 670 680 690 700
VEFNLDDNLF KEVLFEEANY TYQKLMEYNL DFLENKDILA FLEEVENHAK
710 720 730 740 750
KGANIQRYKG LGEMNPNDLW ETTMHKENRS LIKLKIEDLE KTDAVFSLCM
760 770
GDEVEPRRAF IQAHAKDVKQ LDV
Length:773
Mass (Da):87,367
Last modified:November 1, 1997 - v1
Checksum:iFDB47D3112CE8661
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000511 Genomic DNA Translation: AAD07566.1
PIRiE64582
RefSeqiNP_207298.1, NC_000915.1
WP_001182024.1, NC_018939.1

Genome annotation databases

EnsemblBacteriaiAAD07566; AAD07566; HP_0501
GeneIDi900050
KEGGiheo:C694_02575
hpy:HP0501
PATRICifig|85962.47.peg.539

Similar proteinsi

Entry informationi

Entry nameiGYRB_HELPY
AccessioniPrimary (citable) accession number: P55992
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: May 23, 2018
This is version 114 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Helicobacter pylori
    Helicobacter pylori (strain 26695): entries and gene names
  2. SIMILARITY comments
    Index of protein domains and families
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