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P34184

- TOP1_BACPE

UniProt

P34184 - TOP1_BACPE

Protein

DNA topoisomerase 1

Gene

topA

Organism
Bacillus pseudofirmus (strain OF4)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 85 (01 Oct 2014)
      Sequence version 3 (11 Jan 2011)
      Previous versions | rss
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    Functioni

    Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone By similarity.By similarity

    Catalytic activityi

    ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.PROSITE-ProRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei48 – 481Interaction with DNAPROSITE-ProRule annotation
    Sitei167 – 1671Interaction with DNAPROSITE-ProRule annotation
    Sitei171 – 1711Interaction with DNAPROSITE-ProRule annotation
    Active sitei323 – 3231O-(5'-phospho-DNA)-tyrosine intermediateBy similarity
    Sitei325 – 3251Interaction with DNAPROSITE-ProRule annotation
    Sitei529 – 5291Interaction with DNAPROSITE-ProRule annotation

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. DNA topoisomerase type I activity Source: UniProtKB-EC

    GO - Biological processi

    1. DNA topological change Source: InterPro

    Keywords - Molecular functioni

    Isomerase, Topoisomerase

    Keywords - Ligandi

    DNA-binding

    Enzyme and pathway databases

    BioCyciBPSE398511:GJI9-4279-MONOMER.
    BPSE398511:GJI9-4280-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA topoisomerase 1 (EC:5.99.1.2)
    Alternative name(s):
    DNA topoisomerase I
    Omega-protein
    Relaxing enzyme
    Swivelase
    Untwisting enzyme
    Gene namesi
    Name:topA
    Ordered Locus Names:BpOF4_21279/BpOF4_21284
    Encoded oniPlasmid pBpOF4-011 Publication
    OrganismiBacillus pseudofirmus (strain OF4)
    Taxonomic identifieri398511 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    ProteomesiUP000001544: Plasmid pBpOF4-01

    Subcellular locationi

    GO - Cellular componenti

    1. chromosome Source: InterPro

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 706706DNA topoisomerase 1PRO_0000145140Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.By similarity

    Structurei

    3D structure databases

    ProteinModelPortaliP34184.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 140140ToprimPROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni199 – 2046Interaction with DNABy similarity

    Sequence similaritiesi

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

    Family and domain databases

    Gene3Di1.10.290.10. 1 hit.
    1.10.460.10. 2 hits.
    3.40.50.140. 1 hit.
    InterProiIPR000380. Topo_IA.
    IPR003601. Topo_IA_2.
    IPR023406. Topo_IA_AS.
    IPR013497. Topo_IA_cen.
    IPR013824. Topo_IA_cen_sub1.
    IPR013826. Topo_IA_cen_sub3.
    IPR023405. Topo_IA_core_domain.
    IPR003602. Topo_IA_DNA-bd.
    IPR013498. Topo_IA_Znf.
    IPR025589. Toprim_C_rpt.
    IPR006171. Toprim_domain.
    [Graphical view]
    PANTHERiPTHR11390. PTHR11390. 1 hit.
    PfamiPF01131. Topoisom_bac. 1 hit.
    PF01751. Toprim. 1 hit.
    PF13342. Toprim_Crpt. 1 hit.
    PF01396. zf-C4_Topoisom. 1 hit.
    [Graphical view]
    PRINTSiPR00417. PRTPISMRASEI.
    SMARTiSM00437. TOP1Ac. 1 hit.
    SM00436. TOP1Bc. 1 hit.
    SM00493. TOPRIM. 1 hit.
    [Graphical view]
    SUPFAMiSSF56712. SSF56712. 1 hit.
    PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P34184-1 [UniParc]FASTAAdd to Basket

    « Hide

    MYAILAEKPS AAKAYAQALN GKRQGRIYVA PPSSLLPEGA LICAAVGHIL    50
    EFLEPGELNE KYKSYSLDSL PIIIDLFQYK VVSDKKEVLQ RIKDTIFDKR 100
    VKTIILATDA AAEGEYIGRN ILYRLQCKKT IKRLWTSSMT ATSIQKAFSQ 150
    LKADAETLPL YYQAKARAES DYMIGLTLSR AYGILLKEQG IVPHNTTISL 200
    GRVQTPLLAE IVKRERLIEQ FTAENFWTVK ATFNNQGNVY EGEWFHEKEN 250
    RIFKEEQAEQ LCELVRNQSS TIMEMKEEMR TYQPPLLYXL STLQMDAGNA 300
    FGFKPAETLK YAQSLYDKGY LSYPRTQDER ITESDARELE NNIQFLSGHD 350
    TFGALFPLPV STLMNNKRYI GEVTDHHALL ITDKIPKDKD LSEDEKSIYH 400
    LVVKRILAAH YPDVAMSHKE IITKVMDRFT FRSKGKELLS KGWHHIIPPT 450
    NENDIMLPTL LKGSEGVVTD TLTTKSKTKP PNRYTSSSLI GFMKNAAQAI 500
    EDEDRKSISN LPLGTEATRA GLITLLESRK YIEWKKNKVY PTLLGITVVD 550
    SIKRGSVIKS PILTAKWDVK LNEIGASLYN HKDFIAHSKK LSSVLFEEVK 600
    TYSSTWNQNG VERIKSESIG ACLLCGSNVV LRKGKHGEFY GCSNYKDSGC 650
    TFNLPFKVLN KKLSKKQLME LLKNEKTDII KGFKWKDKTF NAPLVWNRED 700
    QKVQFGK 707
    Length:707
    Mass (Da):80,296
    Last modified:January 11, 2011 - v3
    Checksum:i1E07919E5AD9AA00
    GO

    Sequence cautioni

    The sequence ADC52251.1 differs from that shown. Reason: Probable readthrough of the stop codon.
    The sequence CAA78484.1 differs from that shown. Reason: Probable readthrough of the stop codon.
    The sequence CAA78485.1 differs from that shown. Reason: Frameshift at position 525.
    The sequence ADC52252.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.
    The sequence CAA78485.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti126 – 1261Q → H in CAA78484. (PubMed:1329032)Curated
    Sequence conflicti142 – 1421T → F in CAA78484. (PubMed:1329032)Curated
    Sequence conflicti218 – 2181I → L in CAA78484. (PubMed:1329032)Curated
    Sequence conflicti254 – 2541K → T in CAA78484. (PubMed:1329032)Curated
    Sequence conflicti258 – 2581A → D in CAA78484. (PubMed:1329032)Curated
    Sequence conflicti352 – 3521F → S in CAA78485. (PubMed:1329032)Curated
    Sequence conflicti443 – 4431W → R in CAA78485. (PubMed:1329032)Curated
    Sequence conflicti523 – 5242IT → TH in CAA78485. (PubMed:1329032)Curated
    Sequence conflicti548 – 5481V → A in CAA78485. (PubMed:1329032)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001879 Genomic DNA. Translation: ADC52251.1. Sequence problems.
    CP001879 Genomic DNA. Translation: ADC52252.1. Different initiation.
    Z14112 Genomic DNA. Translation: CAA78484.1. Sequence problems.
    Z14112 Genomic DNA. Translation: CAA78485.1. Sequence problems.
    PIRiS23866.
    RefSeqiYP_003429143.1. NC_013792.1.
    YP_003429144.1. NC_013792.1.

    Genome annotation databases

    EnsemblBacteriaiADC52251; ADC52251; BpOF4_21279.
    ADC52252; ADC52252; BpOF4_21284.
    GeneIDi8769255.
    8769256.
    KEGGibpf:BpOF4_21279.
    bpf:BpOF4_21284.
    PATRICi31950839. VBIBacPse80461_4084.

    Keywords - Coding sequence diversityi

    RNA suppression of termination

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001879 Genomic DNA. Translation: ADC52251.1 . Sequence problems.
    CP001879 Genomic DNA. Translation: ADC52252.1 . Different initiation.
    Z14112 Genomic DNA. Translation: CAA78484.1 . Sequence problems.
    Z14112 Genomic DNA. Translation: CAA78485.1 . Sequence problems.
    PIRi S23866.
    RefSeqi YP_003429143.1. NC_013792.1.
    YP_003429144.1. NC_013792.1.

    3D structure databases

    ProteinModelPortali P34184.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ADC52251 ; ADC52251 ; BpOF4_21279 .
    ADC52252 ; ADC52252 ; BpOF4_21284 .
    GeneIDi 8769255.
    8769256.
    KEGGi bpf:BpOF4_21279.
    bpf:BpOF4_21284.
    PATRICi 31950839. VBIBacPse80461_4084.

    Enzyme and pathway databases

    BioCyci BPSE398511:GJI9-4279-MONOMER.
    BPSE398511:GJI9-4280-MONOMER.

    Family and domain databases

    Gene3Di 1.10.290.10. 1 hit.
    1.10.460.10. 2 hits.
    3.40.50.140. 1 hit.
    InterProi IPR000380. Topo_IA.
    IPR003601. Topo_IA_2.
    IPR023406. Topo_IA_AS.
    IPR013497. Topo_IA_cen.
    IPR013824. Topo_IA_cen_sub1.
    IPR013826. Topo_IA_cen_sub3.
    IPR023405. Topo_IA_core_domain.
    IPR003602. Topo_IA_DNA-bd.
    IPR013498. Topo_IA_Znf.
    IPR025589. Toprim_C_rpt.
    IPR006171. Toprim_domain.
    [Graphical view ]
    PANTHERi PTHR11390. PTHR11390. 1 hit.
    Pfami PF01131. Topoisom_bac. 1 hit.
    PF01751. Toprim. 1 hit.
    PF13342. Toprim_Crpt. 1 hit.
    PF01396. zf-C4_Topoisom. 1 hit.
    [Graphical view ]
    PRINTSi PR00417. PRTPISMRASEI.
    SMARTi SM00437. TOP1Ac. 1 hit.
    SM00436. TOP1Bc. 1 hit.
    SM00493. TOPRIM. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56712. SSF56712. 1 hit.
    PROSITEi PS00396. TOPOISOMERASE_I_PROK. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range from 7.5 to 11.4."
      Janto B., Ahmed A., Ito M., Liu J., Hicks D.B., Pagni S., Fackelmayer O.J., Smith T.A., Earl J., Elbourne L.D., Hassan K., Paulsen I.T., Kolsto A.B., Tourasse N.J., Ehrlich G.D., Boissy R., Ivey D.M., Li G.
      , Xue Y., Ma Y., Hu F.Z., Krulwich T.A.
      Environ. Microbiol. 13:3289-3309(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: OF4.
      Plasmid: pBpOF4-01
    2. "A 1.6 kb region of Bacillus firmus OF4 DNA encodes a homolog of Escherichia coli and yeast DNA topoisomerases and may contain a translational readthrough of UGA."
      Ivey D.M., Cheng J., Krulwich T.A.
      Nucleic Acids Res. 20:4928-4928(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 27-706.

    Entry informationi

    Entry nameiTOP1_BACPE
    AccessioniPrimary (citable) accession number: P34184
    Secondary accession number(s): D3G1M5, D3G1M6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1994
    Last sequence update: January 11, 2011
    Last modified: October 1, 2014
    This is version 85 of the entry and version 3 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Caution

    The sequence displayed is the result of a readthrough of the terminator UGA between codons for Tyr-288 and Leu-290. However, translational readthrough of UGA in this protein has not been proven.Curated

    Keywords - Technical termi

    Complete proteome, Plasmid, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3