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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
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 bindingi433 – 4331Magnesium 1; catalyticUniRule annotation
Metal bindingi506 – 5061Magnesium 1; catalyticUniRule annotation
Metal bindingi506 – 5061Magnesium 2UniRule annotation
Metal bindingi508 – 5081Magnesium 2UniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Biological processi

Antibiotic resistance

Keywords - Ligandi

ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciSPNE170187:GHGN-808-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:SP_0806
OrganismiStreptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
Taxonomic identifieri170187 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
Proteomesi
  • UP000000585 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Chemistry

ChEMBLiCHEMBL2311225.
DrugBankiDB01044. Gatifloxacin.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 648648DNA gyrase subunit BPRO_0000145347Add
BLAST

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
Sitei458 – 4581Interaction with DNAUniRule annotation
Sitei461 – 4611Interaction with DNAUniRule annotation

Protein-protein interaction databases

STRINGi170187.SpneT_02000668.

Chemistry

BindingDBiP0A4L9.

Structurei

3D structure databases

ProteinModelPortaliP0A4L9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini427 – 541115ToprimUniRule 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.
HOGENOMiHOG000075154.
KOiK02470.
OMAiIKNMITA.
OrthoDBiEOG6P334W.

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.

P0A4L9-1 [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 LEIVGDTDKT GTTVHFTPDP KIFTETTIFD 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):72,238
Last modified:March 15, 2005 - v1
Checksum:i976A0B030BC892C4
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti88 – 881D → G in CAA58771 (PubMed:7608096).Curated
Sequence conflicti107 – 1071A → S in CAA58771 (PubMed:7608096).Curated
Sequence conflicti304 – 3041D → S in CAA58771 (PubMed:7608096).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti127 – 1271S → L Confers novobiocin resistance.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X83917 Genomic DNA. Translation: CAA58771.1.
AE005672 Genomic DNA. Translation: AAK74943.1.
PIRiF95093.
RefSeqiWP_000134039.1. NZ_AKVY01000001.1.

Genome annotation databases

EnsemblBacteriaiAAK74943; AAK74943; SP_0806.
KEGGispn:SP_0806.
PATRICi19705983. VBIStrPne105772_0838.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X83917 Genomic DNA. Translation: CAA58771.1.
AE005672 Genomic DNA. Translation: AAK74943.1.
PIRiF95093.
RefSeqiWP_000134039.1. NZ_AKVY01000001.1.

3D structure databases

ProteinModelPortaliP0A4L9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi170187.SpneT_02000668.

Chemistry

BindingDBiP0A4L9.
ChEMBLiCHEMBL2311225.
DrugBankiDB01044. Gatifloxacin.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAK74943; AAK74943; SP_0806.
KEGGispn:SP_0806.
PATRICi19705983. VBIStrPne105772_0838.

Phylogenomic databases

eggNOGiENOG4105C7D. Bacteria.
COG0187. LUCA.
HOGENOMiHOG000075154.
KOiK02470.
OMAiIKNMITA.
OrthoDBiEOG6P334W.

Enzyme and pathway databases

BioCyciSPNE170187:GHGN-808-MONOMER.

Miscellaneous databases

PROiP0A4L9.

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

« Hide 'large scale' publications
  1. "Ser-127-to-Leu substitution in the DNA gyrase B subunit of Streptococcus pneumoniae is implicated in novobiocin resistance."
    Munoz R., Bustamante M., de la Campa A.G.
    J. Bacteriol. 177:4166-4170(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 533.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-334 / TIGR4.

Entry informationi

Entry nameiGYRB_STRPN
AccessioniPrimary (citable) accession number: P0A4L9
Secondary accession number(s): P48373
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 15, 2005
Last sequence update: March 15, 2005
Last modified: March 16, 2016
This is version 83 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

Documents

  1. 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.