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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Synechocystis sp. (strain PCC 6803 / Kazusa)
Status
Reviewed-Annotation score: Annotation score: 4 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.By similarity

Catalytic activityi

ATP-dependent breakage, passage and rejoining of double-stranded DNA.PROSITE-ProRule annotation

Cofactori

Mg2+PROSITE-ProRule annotationNote: Binds two Mg2+ per subunit.PROSITE-ProRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi895 – 8951Magnesium 1; catalyticPROSITE-ProRule annotation
Metal bindingi939 – 9391Magnesium 1; catalyticPROSITE-ProRule annotation
Metal bindingi939 – 9391Magnesium 2PROSITE-ProRule annotation
Metal bindingi941 – 9411Magnesium 2PROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

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

Names & Taxonomyi

Protein namesi
Recommended name:
DNA gyrase subunit B (EC:5.99.1.3)
Cleaved into the following chain:
Gene namesi
Name:gyrB
Ordered Locus Names:sll2005
OrganismiSynechocystis sp. (strain PCC 6803 / Kazusa)
Taxonomic identifieri1111708 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechocystis
ProteomesiUP000001425 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 436436DNA gyrase subunit B, 1st partSequence AnalysisPRO_0000034816Add
BLAST
Chaini437 – 871435Ssp gyrB inteinSequence AnalysisPRO_0000034817Add
BLAST
Chaini872 – 1078207DNA gyrase subunit B, 2nd partSequence AnalysisPRO_0000034818Add
BLAST

Post-translational modificationi

This protein undergoes a protein self splicing that involves a post-translational excision of the intervening region (intein) followed by peptide ligation.Curated

Proteomic databases

PaxDbiP77966.
PRIDEiP77966.

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 (By similarity).By similarity

Protein-protein interaction databases

DIPiDIP-48809N.
IntActiP77966. 15 interactions.

Structurei

3D structure databases

ProteinModelPortaliP77966.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini889 – 97486ToprimPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the type II topoisomerase family.Curated
Contains 1 Toprim domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0187.
HOGENOMiHOG000075154.
InParanoidiP77966.
KOiK02470.
OMAiTISHWER.
OrthoDBiEOG6P334W.
PhylomeDBiP77966.

Family and domain databases

Gene3Di2.170.16.10. 2 hits.
3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 2 hits.
InterProiIPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_C.
IPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR030934. Intein_C.
IPR006141. Intein_N.
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.
SM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]
SUPFAMiSSF51294. SSF51294. 2 hits.
SSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 2 hits.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
TIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEiPS50818. INTEIN_C_TER. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P77966-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTMTTTNYGA DQIQVLEGLE PVRKRPGMYI GSTGPKGLHH LVYEVVDNAI
60 70 80 90 100
DEALAGYCTH IEIDINADGS VTVVDNGRGI PTDIHPTTGR SALETVLTVL
110 120 130 140 150
HAGGKFGGGG YKVSGGLHGV GVSVVNALSE WVEVKVWRQG KEHFQRFERG
160 170 180 190 200
NPIGTLEATP NEGHSTGTQV SFLPDTQIFK DGIEFDYHTL ASRLKELAYL
210 220 230 240 250
NAGVRITFGD RRADSLKEEQ FYYEGGIREY VTYMTTDKTP LHEEIIYTSG
260 270 280 290 300
EKNDVQVEVA LQWCVDAYSD TLLGFANNIR TIDGGTHLEG LKAVLTRTLN
310 320 330 340 350
SVARKRNKLK DGDSNLGGEN IREGLTGVIS VKVPDPEFEG QTKTKLGNTE
360 370 380 390 400
VRGIVDTLVG EALTEFLEFN PGVADAIIEK AVQAFKAAEA ARRARELVRR
410 420 430 440 450
KSVLESSTLP GKLADCSSKD PSESEIFIVE GDSAGGCFSG DTLVALTDGR
460 470 480 490 500
SVSFEQLVEE EKQGKQNFCY TIRHDGSIGV EKIINARKTK TNAKVIKVTL
510 520 530 540 550
DNGESIICTP DHKFMLRDGS YKCAMDLTLD DSLMPLHRKI STTEDSGITI
560 570 580 590 600
DGYEMVWSPR SDSWLFTHLV ADWYNRWQGI YIAEEKQHCH HKDFNKRNNN
610 620 630 640 650
PDNLIRLSPE KHLALHRKHI SKTLHRPDVV EKCRRIHQSP EFRRKMSARM
660 670 680 690 700
QSPETRAILS KQAQAQWQNE TYKLTMMESW RSFYDSNEDY RQQNAEQLNR
710 720 730 740 750
AQQEYWAQAE NRTAQAERVR QHFAQNPGLR QQYSENAVKQ WNNPELLKWR
760 770 780 790 800
QKKTKEQWTP EFREKRREAL AQTYYRKTLA ALKQVEIENG YLDISAYDSY
810 820 830 840 850
RISTKDKSLL RFDRFCERYF ENDENLAREA VLNYNHRIVN IEAVSETIDV
860 870 880 890 900
YDIEVPHTHN FALASGVFVH NSAKQGRDRR FQAILPLRGK ILNIEKTDDA
910 920 930 940 950
KIYKNTEIQA LITALGLGIK GDDFDISSLR YHRVVIMTDA DVDGAHIRTL
960 970 980 990 1000
LLTFFYRYQR DLVDQGYIYI ACPPLYKLER GKNHFYCYSD RELQEQISQF
1010 1020 1030 1040 1050
PPNANYTIQR FKGLGEMMPQ QLWDTTMNPE SRTMKRVHIE DAAEADRIFT
1060 1070
VLMGDRVAPR REFIETYGTK LDLTDLDI
Length:1,078
Mass (Da):122,819
Last modified:February 1, 1997 - v1
Checksum:i6CA02586DFEA607B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000022 Genomic DNA. Translation: BAA17720.1.
PIRiS77162.

Genome annotation databases

EnsemblBacteriaiBAA17720; BAA17720; BAA17720.
KEGGisyy:SYNGTS_1144.
syz:MYO_111540.
PATRICi23839370. VBISynSp132158_1249.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000022 Genomic DNA. Translation: BAA17720.1.
PIRiS77162.

3D structure databases

ProteinModelPortaliP77966.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-48809N.
IntActiP77966. 15 interactions.

Proteomic databases

PaxDbiP77966.
PRIDEiP77966.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA17720; BAA17720; BAA17720.
KEGGisyy:SYNGTS_1144.
syz:MYO_111540.
PATRICi23839370. VBISynSp132158_1249.

Phylogenomic databases

eggNOGiCOG0187.
HOGENOMiHOG000075154.
InParanoidiP77966.
KOiK02470.
OMAiTISHWER.
OrthoDBiEOG6P334W.
PhylomeDBiP77966.

Family and domain databases

Gene3Di2.170.16.10. 2 hits.
3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 2 hits.
InterProiIPR002288. DNA_gyrase_B_C.
IPR011557. GyrB.
IPR003594. HATPase_C.
IPR028992. Hedgehog/Intein_dom.
IPR003586. Hint_dom_C.
IPR003587. Hint_dom_N.
IPR030934. Intein_C.
IPR006141. Intein_N.
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.
SM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]
SUPFAMiSSF51294. SSF51294. 2 hits.
SSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 2 hits.
TIGRFAMsiTIGR01059. gyrB. 1 hit.
TIGR01443. intein_Cterm. 1 hit.
TIGR01445. intein_Nterm. 1 hit.
PROSITEiPS50818. INTEIN_C_TER. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions."
    Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y., Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T., Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S.
    , Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
    DNA Res. 3:109-136(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: PCC 6803 / Kazusa.

Entry informationi

Entry nameiGYRB_SYNY3
AccessioniPrimary (citable) accession number: P77966
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: February 1, 1997
Last modified: July 22, 2015
This is version 119 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. Intein-containing proteins
    List of intein-containing protein entries
  2. SIMILARITY comments
    Index of protein domains and families
  3. Synechocystis PCC 6803
    Synechocystis (strain PCC 6803): entries and gene names

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.