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Q54RC3

- TOP1_DICDI

UniProt

Q54RC3 - TOP1_DICDI

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Protein

DNA topoisomerase 1

Gene

top1

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi

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
Complete GO annotation...

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
Complete GO annotation...

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.
InParanoidiQ54RC3.
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

        10         20         30         40         50
MEVKQEILTP MKVEKTNGNV PTPPPTTTTT TVMDDDLFDD EASPPQPNKK
60 70 80 90 100
LKAENGSIKK LTPTPKPAPV TPKPTAAVNG KKPIPKKKPV DSSSDSDSSD
110 120 130 140 150
SSSDSDSDSS DSDSDSSSSD SSSSDSDVPK KKPISKIPNK PSGTVSKTSK
160 170 180 190 200
NSPKTTTTTT TTTTTVKSKP APKVKPEQSS SDDSSSDSSD DSSDDSSSDS
210 220 230 240 250
SSEEEKPKKK PSKKPAAVKK EITVKKETTT TTKKTPVKKE VEVKKETKTT
260 270 280 290 300
TTKKVKKEES DDDGEDEKTT TKKKTTTRKR KLKEEEEGEE EEEEGVNKWW
310 320 330 340 350
DKEDDEDDGT KWTTLIHNGP VFPPAYVPHG IKFMYDGKVV KLTPKQEEVA
360 370 380 390 400
TFYANYLETD HVKKQAFKDN FFKEFKGLLT SEQKEIVKKM DKCDFSHIHT
410 420 430 440 450
HLKTKKEQRK ARSKEEKDAE TAEKKKIQEK HGFATIDGFK EKVGNYMIEP
460 470 480 490 500
PGLFLGRGQH PKTGMLKQRI MPSDVTLNIG EGEVIPPSPI PGEKWKEIVH
510 520 530 540 550
NNTVTWLAFW RESVNGGFKY VWLAPSSKIK GQADRKKFEV ARGLKNCIGD
560 570 580 590 600
IRKGYQKSFN DESTEKRQLA VALYLIDFLA LRVGNEKGED QADTVGCCSL
610 620 630 640 650
RVEHIKLESN NTITLDFLGK DSMRYLNTVQ IREDAYKVLK TFVKGKKPTD
660 670 680 690 700
LLFDSLTVTQ LNNHLKKQMT GLSAKVFRTY NASITLQKEL DKMDTKEFQS
710 720 730 740 750
IDEKILFYNR CNREVAILCN HQKAPPKNLA ETMSKIDEKI QELRDLQDLC
760 770 780 790 800
RIKIGKTPKS QQEDIESREA ERLPKLIQLA ITNKKDKDKE KTDKEISFDV
810 820 830 840 850
KAAFEKSRTL PDAKGKIKEK IAKYEEQIKK QEILKTGKDE LKTVALGTSK
860 870 880 890
INYLDPRITV AWCKKNKVPV DKIFTKSLRD KFPWSDVGTD YIF
Length:893
Mass (Da):100,612
Last modified:May 24, 2005 - v1
Checksum:iDD9BB5F99BF3331E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.
InParanoidi Q54RC3.
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 29, 2014
This is version 69 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