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Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Synechocystis sp. (strain PCC 6803 / Kazusa)
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.By similarity

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.Curated

Catalytic activityi

ATP-dependent breakage, passage and rejoining of double-stranded DNA.By similarity

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi895Magnesium 1; catalyticPROSITE-ProRule annotation1
Metal bindingi939Magnesium 1; catalyticPROSITE-ProRule annotation1
Metal bindingi939Magnesium 2PROSITE-ProRule annotation1
Metal bindingi941Magnesium 2PROSITE-ProRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionIsomerase, Topoisomerase
LigandATP-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 lineageiBacteriaCyanobacteriaSynechococcalesMerismopediaceaeSynechocystis
Proteomesi
  • UP000001425 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm By similarity

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004355391 – 1078DNA gyrase subunit BAdd BLAST1078
ChainiPRO_00000348161 – 436DNA gyrase subunit B, 1st partAdd BLAST436
ChainiPRO_0000034817437 – 871Ssp GyrB inteinAdd BLAST435
ChainiPRO_0000034818872 – 1078DNA gyrase subunit B, 2nd partAdd BLAST207

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

PRIDEiP77966.

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.By similarity

Protein-protein interaction databases

DIPiDIP-48809N.
IntActiP77966. 15 interactors.
STRINGi1148.SYNGTS_1144.

Structurei

3D structure databases

ProteinModelPortaliP77966.
SMRiP77966.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini889 – 974ToprimPROSITE-ProRule annotationAdd BLAST86

Sequence similaritiesi

Belongs to the type II topoisomerase GyrB family.Curated

Phylogenomic databases

HOGENOMiHOG000075154.
InParanoidiP77966.
KOiK02470.
OMAiDCSSRDP.
PhylomeDBiP77966.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 2 hits.
InterProiView protein in InterPro
IPR002288. 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.
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.
PRINTSiPR00418. TPI2FAMILY.
SMARTiView protein in SMART
SM00387. HATPase_c. 1 hit.
SM00305. HintC. 1 hit.
SM00306. HintN. 1 hit.
SM00433. TOP2c. 1 hit.
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.
PROSITEiView protein in PROSITE
PS50818. INTEIN_C_TER. 1 hit.
PS50817. INTEIN_N_TER. 1 hit.
PS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.

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.
KEGGisyn:sll2005.

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.

Entry informationi

Entry nameiGYRB_SYNY3
AccessioniPrimary (citable) accession number: P77966
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: February 1, 1997
Last modified: July 5, 2017
This is version 132 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. 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