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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

DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings, including catenanes and knotted rings.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 Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) or Ca2+.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi422 – 4221Magnesium 1; catalyticUniRule annotation
Sitei447 – 4471Interaction with DNAUniRule annotation
Sitei450 – 4501Interaction with DNAUniRule annotation
Metal bindingi495 – 4951Magnesium 1; catalyticUniRule annotation
Metal bindingi495 – 4951Magnesium 2UniRule annotation
Metal bindingi497 – 4971Magnesium 2UniRule annotation

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-HAMAP
  2. DNA binding Source: UniProtKB-HAMAP
  3. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: UniProtKB-HAMAP
  4. magnesium ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. DNA-dependent DNA replication Source: UniProtKB-HAMAP
  2. DNA topological change Source: InterPro
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
ProteomesiUP000000429: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. chromosome Source: InterPro
  2. cytoplasm Source: UniProtKB-SubCell
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

PRIDEiP55992.

Interactioni

Subunit structurei

Heterotetramer, composed of two GyrA and two GyrB chains. Within the heterotetramer, GyrA contains the active site tyrosine that forms a covalent intermediate with the DNA, while GyrB contributes the cofactor binding sites and catalyzes ATP hydrolysis.UniRule 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 family.UniRule annotation
Contains 1 Toprim domain.UniRule annotation

Phylogenomic databases

eggNOGiCOG0187.
KOiK02470.
OMAiIFETTEF.
OrthoDBiEOG6P334W.

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.
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.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_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.
YP_006934423.1. NC_018939.1.

Genome annotation databases

EnsemblBacteriaiAAD07566; AAD07566; HP_0501.
GeneIDi13869691.
900050.
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.
YP_006934423.1. NC_018939.1.

3D structure databases

ProteinModelPortaliP55992.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Proteomic databases

PRIDEiP55992.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD07566; AAD07566; HP_0501.
GeneIDi13869691.
900050.
KEGGiheo:C694_02575.
hpy:HP0501.
PATRICi20592277. VBIHelPyl33062_0527.

Phylogenomic databases

eggNOGiCOG0187.
KOiK02470.
OMAiIFETTEF.
OrthoDBiEOG6P334W.

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.
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.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_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...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700392 / 26695.

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: January 7, 2015
This is version 98 of the entry and version 1 of the sequence. [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

External Data

Dasty 3

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 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.