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P0C559

- GYRB_MYCSM

UniProt

P0C559 - GYRB_MYCSM

Protein

DNA gyrase subunit B

Gene

gyrB

Organism
Mycobacterium smegmatis
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 41 (01 Oct 2014)
      Sequence version 1 (10 Jul 2007)
      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.

    Catalytic activityi

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

    Cofactori

    Magnesium. 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+ and Ca2+.UniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi459 – 4591Magnesium 1; catalyticUniRule annotation
    Sitei484 – 4841Interaction with DNAUniRule annotation
    Sitei487 – 4871Interaction with DNAUniRule annotation
    Metal bindingi532 – 5321Magnesium 1; catalyticUniRule annotation
    Metal bindingi532 – 5321Magnesium 2UniRule annotation
    Metal bindingi534 – 5341Magnesium 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

    Keywords - Molecular functioni

    Isomerase, Topoisomerase

    Keywords - Ligandi

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

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA gyrase subunit BUniRule annotation (EC:5.99.1.3UniRule annotation)
    Gene namesi
    Name:gyrBUniRule annotation
    OrganismiMycobacterium smegmatis
    Taxonomic identifieri1772 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacterium

    Subcellular locationi

    Cytoplasm UniRule annotation

    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
    Initiator methioninei1 – 11RemovedBy similarity
    Chaini2 – 675674DNA gyrase subunit BPRO_0000145324Add
    BLAST

    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

    Structurei

    Secondary structure

    1
    675
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi24 – 285
    Helixi31 – 344
    Helixi39 – 5820
    Beta strandi64 – 696
    Beta strandi73 – 797
    Beta strandi90 – 945
    Helixi95 – 1017
    Helixi127 – 1304
    Beta strandi131 – 14111
    Beta strandi144 – 1518
    Beta strandi159 – 1635
    Beta strandi168 – 1758
    Turni177 – 1793
    Helixi187 – 20014
    Beta strandi205 – 2106
    Turni211 – 2133
    Beta strandi248 – 2514

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4B6CX-ray2.20A/B9-255[»]
    4BAEX-ray2.35A/B/C/D19-212[»]
    A/B/C/D247-255[»]
    ProteinModelPortaliP0C559.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini453 – 567115ToprimUniRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the type II topoisomerase family.UniRule annotation
    Contains 1 Toprim domain.UniRule annotation

    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_ATP-bd.
    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. 1 hit.
    TIGRFAMsiTIGR01059. gyrB. 1 hit.
    PROSITEiPS00177. 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.

    P0C559-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAAQKNNAPK EYGADSITIL EGLEAVRKRP GMYIGSTGER GLHHLIWEVV    50
    DNAVDEAMAG FATRVDVKIH ADGSVEVRDD GRGIPVEMHA TGMPTIDVVM 100
    TQLHAGGKFD GETYAVSGGL HGVGVSVVNA LSTRLEATVL RDGYEWFQYY 150
    DRSVPGKLKQ GGETKETGTT IRFWADPEIF ETTDYNFETV ARRLQEMAFL 200
    NKGLTIELTD ERVTAEEVVD DVVKDTAEAP KTADEKAAEA TGPSKVKHRV 250
    FHYPGGLVDY VKHINRTKTP IQQSIIDFDG KGPGHEVEIA MQWNAGYSES 300
    VHTFANTINT HEGGTHEEGF RAALTSVVNR YAKDKKLLKD KDPNLTGDDI 350
    REGLAAVISV KVAEPQFEGQ TKTKLGNTEV KSFVQKICNE QLQHWFEANP 400
    AEAKTVVNKA VSSAQARIAA RKARELVRRK SATDIGGLPG KLADCRSTDP 450
    SKSELYVVEG DSAGGSAKSG RDSMFQAILP LRGKIINVEK ARIDRVLKNT 500
    EVQSIITALG TGIHDEFDIS KLRYHKIVLM ADADVDGQHI STLLLTLLFR 550
    FMKPLVENGH IFLAQPPLYK LKWQRSEPEF AYSDRERDGL LEAGRAAGKK 600
    INVDDGIQRY KGLGEMDAKE LWETTMDPSV RVLRQVTLDD AAAADELFSI 650
    LMGEDVEARR SFITRNAKDV RFLDV 675
    Length:675
    Mass (Da):74,512
    Last modified:July 10, 2007 - v1
    Checksum:i68A9B7F98BE07951
    GO

    Sequence cautioni

    The sequence CAA63253.1 differs from that shown. Reason: Erroneous initiation.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti162 – 1621G → R in CAA58884. (PubMed:8574396)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X92503 Genomic DNA. Translation: CAA63253.1. Different initiation.
    X84077 Genomic DNA. Translation: CAA58884.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X92503 Genomic DNA. Translation: CAA63253.1 . Different initiation.
    X84077 Genomic DNA. Translation: CAA58884.1 .

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4B6C X-ray 2.20 A/B 9-255 [» ]
    4BAE X-ray 2.35 A/B/C/D 19-212 [» ]
    A/B/C/D 247-255 [» ]
    ProteinModelPortali P0C559.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Family and domain databases

    Gene3Di 3.30.230.10. 1 hit.
    3.30.565.10. 1 hit.
    3.40.50.670. 1 hit.
    HAMAPi MF_01898. GyrB.
    InterProi IPR002288. DNA_gyrase_B_C.
    IPR011557. GyrB.
    IPR003594. HATPase_ATP-bd.
    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.
    SM00433. TOP2c. 1 hit.
    [Graphical view ]
    SUPFAMi SSF54211. SSF54211. 1 hit.
    SSF55874. SSF55874. 1 hit.
    SSF56719. SSF56719. 1 hit.
    TIGRFAMsi TIGR01059. gyrB. 1 hit.
    PROSITEi PS00177. TOPOISOMERASE_II. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Organization of the origins of replication of the chromosomes of Mycobacterium smegmatis, Mycobacterium leprae and Mycobacterium tuberculosis and isolation of a functional origin from M. smegmatis."
      Salazar L., Fsihi H., De Rossi E., Riccardi G., Rios C., Cole S.T., Takiff H.E.
      Mol. Microbiol. 20:283-293(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 607 / DSM 43465 / JCM 20379 / NBRC 3207 / NRRL B-692.
    2. "Mycobacterium smegmatis DNA gyrase: cloning and overexpression in Escherichia coli."
      Madhusudan K., Nagaraja V.
      Microbiology 141:3029-3037(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: SN2.

    Entry informationi

    Entry nameiGYRB_MYCSM
    AccessioniPrimary (citable) accession number: P0C559
    Secondary accession number(s): P48355, Q59555
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 10, 2007
    Last sequence update: July 10, 2007
    Last modified: October 1, 2014
    This is version 41 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

    3D-structure

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3