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P77966

- GYRB_SYNY3

UniProt

P77966 - GYRB_SYNY3

Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Synechocystis sp. (strain PCC 6803 / Kazusa)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 111 (01 Oct 2014)
      Sequence version 1 (01 Feb 1997)
      Previous versions | rss
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    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

    Magnesium. 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

    1. ATP binding Source: UniProtKB-KW
    2. DNA binding Source: InterPro
    3. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: UniProtKB-EC
    4. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. DNA topological change Source: InterPro
    2. intein-mediated protein splicing Source: InterPro

    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: Chromosome

    Subcellular locationi

    Cytoplasm Curated

    GO - Cellular componenti

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

    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.
    STRINGi1148.sll2005.

    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.
    KOiK02470.
    OMAiNARWREV.
    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_ATP-bd.
    IPR028992. Hedgehog/Intein_dom.
    IPR003586. Hint_dom_C.
    IPR003587. Hint_dom_N.
    IPR006141. Intein_splice_site.
    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.
    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

    MTMTTTNYGA DQIQVLEGLE PVRKRPGMYI GSTGPKGLHH LVYEVVDNAI     50
    DEALAGYCTH IEIDINADGS VTVVDNGRGI PTDIHPTTGR SALETVLTVL 100
    HAGGKFGGGG YKVSGGLHGV GVSVVNALSE WVEVKVWRQG KEHFQRFERG 150
    NPIGTLEATP NEGHSTGTQV SFLPDTQIFK DGIEFDYHTL ASRLKELAYL 200
    NAGVRITFGD RRADSLKEEQ FYYEGGIREY VTYMTTDKTP LHEEIIYTSG 250
    EKNDVQVEVA LQWCVDAYSD TLLGFANNIR TIDGGTHLEG LKAVLTRTLN 300
    SVARKRNKLK DGDSNLGGEN IREGLTGVIS VKVPDPEFEG QTKTKLGNTE 350
    VRGIVDTLVG EALTEFLEFN PGVADAIIEK AVQAFKAAEA ARRARELVRR 400
    KSVLESSTLP GKLADCSSKD PSESEIFIVE GDSAGGCFSG DTLVALTDGR 450
    SVSFEQLVEE EKQGKQNFCY TIRHDGSIGV EKIINARKTK TNAKVIKVTL 500
    DNGESIICTP DHKFMLRDGS YKCAMDLTLD DSLMPLHRKI STTEDSGITI 550
    DGYEMVWSPR SDSWLFTHLV ADWYNRWQGI YIAEEKQHCH HKDFNKRNNN 600
    PDNLIRLSPE KHLALHRKHI SKTLHRPDVV EKCRRIHQSP EFRRKMSARM 650
    QSPETRAILS KQAQAQWQNE TYKLTMMESW RSFYDSNEDY RQQNAEQLNR 700
    AQQEYWAQAE NRTAQAERVR QHFAQNPGLR QQYSENAVKQ WNNPELLKWR 750
    QKKTKEQWTP EFREKRREAL AQTYYRKTLA ALKQVEIENG YLDISAYDSY 800
    RISTKDKSLL RFDRFCERYF ENDENLAREA VLNYNHRIVN IEAVSETIDV 850
    YDIEVPHTHN FALASGVFVH NSAKQGRDRR FQAILPLRGK ILNIEKTDDA 900
    KIYKNTEIQA LITALGLGIK GDDFDISSLR YHRVVIMTDA DVDGAHIRTL 950
    LLTFFYRYQR DLVDQGYIYI ACPPLYKLER GKNHFYCYSD RELQEQISQF 1000
    PPNANYTIQR FKGLGEMMPQ QLWDTTMNPE SRTMKRVHIE DAAEADRIFT 1050
    VLMGDRVAPR REFIETYGTK LDLTDLDI 1078
    Length:1,078
    Mass (Da):122,819
    Last modified:February 1, 1997 - v1
    Checksum:i6CA02586DFEA607B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000022 Genomic DNA. Translation: BAA17720.1.
    PIRiS77162.
    RefSeqiNP_441040.1. NC_000911.1.
    YP_005651097.1. NC_017277.1.
    YP_007450922.1. NC_020286.1.

    Genome annotation databases

    EnsemblBacteriaiBAA17720; BAA17720; BAA17720.
    GeneIDi954353.
    KEGGisyn:sll2005.
    syy:SYNGTS_1144.
    syz:MYO_111540.
    PATRICi23839370. VBISynSp132158_1249.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000022 Genomic DNA. Translation: BAA17720.1 .
    PIRi S77162.
    RefSeqi NP_441040.1. NC_000911.1.
    YP_005651097.1. NC_017277.1.
    YP_007450922.1. NC_020286.1.

    3D structure databases

    ProteinModelPortali P77966.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-48809N.
    IntActi P77966. 15 interactions.
    STRINGi 1148.sll2005.

    Proteomic databases

    PaxDbi P77966.
    PRIDEi P77966.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAA17720 ; BAA17720 ; BAA17720 .
    GeneIDi 954353.
    KEGGi syn:sll2005.
    syy:SYNGTS_1144.
    syz:MYO_111540.
    PATRICi 23839370. VBISynSp132158_1249.

    Phylogenomic databases

    eggNOGi COG0187.
    HOGENOMi HOG000075154.
    KOi K02470.
    OMAi NARWREV.
    OrthoDBi EOG6P334W.
    PhylomeDBi P77966.

    Family and domain databases

    Gene3Di 2.170.16.10. 2 hits.
    3.30.230.10. 1 hit.
    3.30.565.10. 1 hit.
    3.40.50.670. 2 hits.
    InterProi IPR002288. DNA_gyrase_B_C.
    IPR011557. GyrB.
    IPR003594. HATPase_ATP-bd.
    IPR028992. Hedgehog/Intein_dom.
    IPR003586. Hint_dom_C.
    IPR003587. Hint_dom_N.
    IPR006141. Intein_splice_site.
    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 ]
    Pfami PF00204. DNA_gyraseB. 1 hit.
    PF00986. DNA_gyraseB_C. 1 hit.
    PF02518. HATPase_c. 1 hit.
    PF01751. Toprim. 1 hit.
    [Graphical view ]
    PRINTSi PR00418. TPI2FAMILY.
    SMARTi SM00387. HATPase_c. 1 hit.
    SM00305. HintC. 1 hit.
    SM00306. HintN. 1 hit.
    SM00433. TOP2c. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51294. SSF51294. 2 hits.
    SSF54211. SSF54211. 1 hit.
    SSF55874. SSF55874. 1 hit.
    SSF56719. SSF56719. 2 hits.
    TIGRFAMsi TIGR01059. gyrB. 1 hit.
    TIGR01443. intein_Cterm. 1 hit.
    TIGR01445. intein_Nterm. 1 hit.
    PROSITEi PS50818. INTEIN_C_TER. 1 hit.
    PS50817. INTEIN_N_TER. 1 hit.
    PS00177. TOPOISOMERASE_II. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    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: October 1, 2014
    This is version 111 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