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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
Status
Reviewed-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 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 bindingi422 – 4221Magnesium 1; catalyticUniRule annotation
Metal bindingi495 – 4951Magnesium 1; catalyticUniRule annotation
Metal bindingi495 – 4951Magnesium 2UniRule annotation
Metal bindingi497 – 4971Magnesium 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

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

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 773773DNA gyrase subunit BPRO_0000145314Add
BLAST

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)LengthDescriptionGraphical viewFeature identifierActions
Sitei447 – 4471Interaction with DNAUniRule annotation
Sitei450 – 4501Interaction with DNAUniRule annotation

Protein-protein interaction databases

DIPiDIP-3593N.
IntActiP55992. 3 interactions.
MINTiMINT-168943.
STRINGi85962.HP0501.

Structurei

3D structure databases

ProteinModelPortaliP55992.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini416 – 530115ToprimUniRule 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.
KOiK02470.
OMAiIKNMITA.

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. 1 hit.
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. 2 hits.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

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.
PATRICi20592277. VBIHelPyl33062_0527.

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliP55992.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-3593N.
IntActiP55992. 3 interactions.
MINTiMINT-168943.
STRINGi85962.HP0501.

Proteomic databases

PaxDbiP55992.
PRIDEiP55992.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD07566; AAD07566; HP_0501.
GeneIDi900050.
KEGGiheo:C694_02575.
hpy:HP0501.
PATRICi20592277. VBIHelPyl33062_0527.

Phylogenomic databases

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

Enzyme and pathway databases

BioCyciHPY:HP0501-MONOMER.

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. 1 hit.
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. 2 hits.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiGYRB_HELPY
AccessioniPrimary (citable) accession number: P55992
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: September 7, 2016
This is version 105 of the entry and version 1 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. Helicobacter pylori
    Helicobacter pylori (strain 26695): entries and gene names
  2. 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.