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Q54RC3

- TOP1_DICDI

UniProt

Q54RC3 - TOP1_DICDI

Protein

DNA topoisomerase 1

Gene

top1

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 68 (01 Oct 2014)
      Sequence version 1 (24 May 2005)
      Previous versions | rss
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    Functioni

    Releases the supercoiling and torsional tension of DNA 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-(3'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 5'-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 5'-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
    Sitei409 – 4091Interaction with DNABy similarity
    Sitei457 – 4571Interaction with DNABy similarity
    Sitei506 – 5061Interaction with DNABy similarity
    Sitei537 – 5371Interaction with DNABy similarity
    Sitei594 – 5941Interaction with DNABy similarity
    Sitei620 – 6201Interaction with DNABy similarity
    Sitei662 – 6621Interaction with DNABy similarity
    Sitei721 – 7211Interaction with DNABy similarity
    Sitei739 – 7391Interaction with DNABy similarity
    Active sitei853 – 8531O-(3'-phospho-DNA)-tyrosine intermediatePROSITE-ProRule annotation

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. DNA topoisomerase type I activity Source: dictyBase
    3. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: InterPro

    GO - Biological processi

    1. chromatin remodeling Source: RefGenome
    2. chromosome segregation Source: RefGenome
    3. DNA replication Source: dictyBase
    4. DNA topological change Source: dictyBase

    Keywords - Molecular functioni

    Isomerase, Topoisomerase

    Keywords - Ligandi

    DNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA topoisomerase 1 (EC:5.99.1.2)
    Alternative name(s):
    DNA topoisomerase I
    Gene namesi
    Name:top1
    ORF Names:DDB_G0283205
    OrganismiDictyostelium discoideum (Slime mold)
    Taxonomic identifieri44689 [NCBI]
    Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
    ProteomesiUP000002195: Chromosome 4, UP000002195: Unassembled WGS sequence

    Organism-specific databases

    dictyBaseiDDB_G0283205. top1.

    Subcellular locationi

    Nucleus By similarity

    GO - Cellular componenti

    1. nucleolus Source: RefGenome
    2. nucleus Source: dictyBase
    3. replication fork protection complex Source: RefGenome

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 893893DNA topoisomerase 1PRO_0000330481Add
    BLAST

    Proteomic databases

    PRIDEiQ54RC3.

    Interactioni

    Protein-protein interaction databases

    STRINGi44689.DDBDRAFT_0185416.

    Structurei

    3D structure databases

    ProteinModelPortaliQ54RC3.
    SMRiQ54RC3. Positions 847-885.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni519 – 5202Interaction with DNABy similarity
    Regioni582 – 5876Interaction with DNABy similarity
    Regioni673 – 6753Interaction with DNABy similarity

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi26 – 316Poly-Thr
    Compositional biasi92 – 202111Ser-richAdd
    BLAST
    Compositional biasi144 – 16522Thr-richAdd
    BLAST
    Compositional biasi223 – 27755Thr-richAdd
    BLAST
    Compositional biasi284 – 29411Poly-GluAdd
    BLAST

    Sequence similaritiesi

    Belongs to the type IB topoisomerase family.Curated

    Phylogenomic databases

    eggNOGiCOG3569.
    KOiK03163.
    OMAiREKFNWA.
    PhylomeDBiQ54RC3.

    Family and domain databases

    Gene3Di1.10.10.41. 1 hit.
    1.10.132.10. 2 hits.
    2.170.11.10. 2 hits.
    3.90.15.10. 1 hit.
    InterProiIPR011010. DNA_brk_join_enz.
    IPR013034. DNA_topo_domain1.
    IPR001631. TopoI.
    IPR018521. TopoI_AS.
    IPR025834. TopoI_C_dom.
    IPR014711. TopoI_cat_a-hlx-sub_euk.
    IPR014727. TopoI_cat_a/b-sub_euk.
    IPR013500. TopoI_cat_euk.
    IPR008336. TopoI_DNA-bd_euk.
    IPR013030. TopoI_DNA-bd_mixed-a/b_euk.
    IPR013499. TopoI_euk.
    [Graphical view]
    PfamiPF14370. Topo_C_assoc. 1 hit.
    PF01028. Topoisom_I. 1 hit.
    PF02919. Topoisom_I_N. 1 hit.
    [Graphical view]
    PRINTSiPR00416. EUTPISMRASEI.
    SMARTiSM00435. TOPEUc. 1 hit.
    [Graphical view]
    SUPFAMiSSF56349. SSF56349. 2 hits.
    SSF56741. SSF56741. 1 hit.
    PROSITEiPS00176. TOPOISOMERASE_I_EUK. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q54RC3-1 [UniParc]FASTAAdd to Basket

    « Hide

    MEVKQEILTP MKVEKTNGNV PTPPPTTTTT TVMDDDLFDD EASPPQPNKK    50
    LKAENGSIKK LTPTPKPAPV TPKPTAAVNG KKPIPKKKPV DSSSDSDSSD 100
    SSSDSDSDSS DSDSDSSSSD SSSSDSDVPK KKPISKIPNK PSGTVSKTSK 150
    NSPKTTTTTT TTTTTVKSKP APKVKPEQSS SDDSSSDSSD DSSDDSSSDS 200
    SSEEEKPKKK PSKKPAAVKK EITVKKETTT TTKKTPVKKE VEVKKETKTT 250
    TTKKVKKEES DDDGEDEKTT TKKKTTTRKR KLKEEEEGEE EEEEGVNKWW 300
    DKEDDEDDGT KWTTLIHNGP VFPPAYVPHG IKFMYDGKVV KLTPKQEEVA 350
    TFYANYLETD HVKKQAFKDN FFKEFKGLLT SEQKEIVKKM DKCDFSHIHT 400
    HLKTKKEQRK ARSKEEKDAE TAEKKKIQEK HGFATIDGFK EKVGNYMIEP 450
    PGLFLGRGQH PKTGMLKQRI MPSDVTLNIG EGEVIPPSPI PGEKWKEIVH 500
    NNTVTWLAFW RESVNGGFKY VWLAPSSKIK GQADRKKFEV ARGLKNCIGD 550
    IRKGYQKSFN DESTEKRQLA VALYLIDFLA LRVGNEKGED QADTVGCCSL 600
    RVEHIKLESN NTITLDFLGK DSMRYLNTVQ IREDAYKVLK TFVKGKKPTD 650
    LLFDSLTVTQ LNNHLKKQMT GLSAKVFRTY NASITLQKEL DKMDTKEFQS 700
    IDEKILFYNR CNREVAILCN HQKAPPKNLA ETMSKIDEKI QELRDLQDLC 750
    RIKIGKTPKS QQEDIESREA ERLPKLIQLA ITNKKDKDKE KTDKEISFDV 800
    KAAFEKSRTL PDAKGKIKEK IAKYEEQIKK QEILKTGKDE LKTVALGTSK 850
    INYLDPRITV AWCKKNKVPV DKIFTKSLRD KFPWSDVGTD YIF 893
    Length:893
    Mass (Da):100,612
    Last modified:May 24, 2005 - v1
    Checksum:iDD9BB5F99BF3331E
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AAFI02000051 Genomic DNA. Translation: EAL65841.1.
    RefSeqiXP_639222.1. XM_634130.1.

    Genome annotation databases

    EnsemblProtistsiDDB0234191; DDB0234191; DDB_G0283205.
    GeneIDi8623995.
    KEGGiddi:DDB_G0283205.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AAFI02000051 Genomic DNA. Translation: EAL65841.1 .
    RefSeqi XP_639222.1. XM_634130.1.

    3D structure databases

    ProteinModelPortali Q54RC3.
    SMRi Q54RC3. Positions 847-885.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 44689.DDBDRAFT_0185416.

    Proteomic databases

    PRIDEi Q54RC3.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblProtistsi DDB0234191 ; DDB0234191 ; DDB_G0283205 .
    GeneIDi 8623995.
    KEGGi ddi:DDB_G0283205.

    Organism-specific databases

    dictyBasei DDB_G0283205. top1.

    Phylogenomic databases

    eggNOGi COG3569.
    KOi K03163.
    OMAi REKFNWA.
    PhylomeDBi Q54RC3.

    Family and domain databases

    Gene3Di 1.10.10.41. 1 hit.
    1.10.132.10. 2 hits.
    2.170.11.10. 2 hits.
    3.90.15.10. 1 hit.
    InterProi IPR011010. DNA_brk_join_enz.
    IPR013034. DNA_topo_domain1.
    IPR001631. TopoI.
    IPR018521. TopoI_AS.
    IPR025834. TopoI_C_dom.
    IPR014711. TopoI_cat_a-hlx-sub_euk.
    IPR014727. TopoI_cat_a/b-sub_euk.
    IPR013500. TopoI_cat_euk.
    IPR008336. TopoI_DNA-bd_euk.
    IPR013030. TopoI_DNA-bd_mixed-a/b_euk.
    IPR013499. TopoI_euk.
    [Graphical view ]
    Pfami PF14370. Topo_C_assoc. 1 hit.
    PF01028. Topoisom_I. 1 hit.
    PF02919. Topoisom_I_N. 1 hit.
    [Graphical view ]
    PRINTSi PR00416. EUTPISMRASEI.
    SMARTi SM00435. TOPEUc. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56349. SSF56349. 2 hits.
    SSF56741. SSF56741. 1 hit.
    PROSITEi PS00176. TOPOISOMERASE_I_EUK. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The genome of the social amoeba Dictyostelium discoideum."
      Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N.
      , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.
      Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: AX4.

    Entry informationi

    Entry nameiTOP1_DICDI
    AccessioniPrimary (citable) accession number: Q54RC3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 29, 2008
    Last sequence update: May 24, 2005
    Last modified: October 1, 2014
    This is version 68 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)

    Miscellaneousi

    Miscellaneous

    Eukaryotic topoisomerase I and II can relax both negative and positive supercoils, whereas prokaryotic enzymes relax only negative supercoils.By similarity

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Dictyostelium discoideum
      Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3