Q54RC3 (TOP1_DICDI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA topoisomerase 1
EC=5.99.1.2

Alternative name(s):
DNA topoisomerase I

Gene names

Name:	top1
ORF Names:	DDB_G0283205

Organism

Dictyostelium discoideum (Slime mold)

Taxonomic identifier

44689 [NCBI]

Taxonomic lineage

Eukaryota › Amoebozoa › Mycetozoa › Dictyosteliida › Dictyostelium

Protein attributes

Sequence length	893 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	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 than 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.
Catalytic activity	ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.
Subcellular location	Nucleus By similarity.
Miscellaneous	Eukaryotic topoisomerase I and II can relax both negative and positive supercoils, whereas prokaryotic enzymes relax only negative supercoils By similarity.
Sequence similarities	Belongs to the type IB topoisomerase family.

Ontologies

Keywords
Cellular component	Nucleus
Ligand	ATP-binding DNA-binding Nucleotide-binding
Molecular function	Isomerase Topoisomerase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	DNA replication Inferred from sequence or structural similarity. Source: dictyBase DNA topological change Inferred from sequence or structural similarity. Source: dictyBase
Cellular component	chromosome Inferred from electronic annotation. Source: InterPro nucleus Inferred from sequence or structural similarity. Source: dictyBase
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA topoisomerase (ATP-hydrolyzing) activity Inferred from electronic annotation. Source: InterPro DNA topoisomerase type I activity Inferred from sequence or structural similarity. Source: dictyBase chromatin DNA binding Inferred from Biological aspect of Ancestor. Source: RefGenome
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 893	893	DNA topoisomerase 1		PRO_0000330481
Regions
	Compositional bias	26 – 31	6	Poly-Thr
	Compositional bias	92 – 202	111	Ser-rich
	Compositional bias	144 – 165	22	Thr-rich
	Compositional bias	223 – 277	55	Thr-rich
	Compositional bias	284 – 294	11	Poly-Glu
Sites
	Active site	853	1	O-(3'-phospho-DNA)-tyrosine intermediate By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q54RC3 [UniParc]. Last modified May 24, 2005. Version 1. Checksum: DD9BB5F99BF3331E	FASTA	893	100,612
	10 20 30 40 50 60 MEVKQEILTP MKVEKTNGNV PTPPPTTTTT TVMDDDLFDD EASPPQPNKK LKAENGSIKK 70 80 90 100 110 120 LTPTPKPAPV TPKPTAAVNG KKPIPKKKPV DSSSDSDSSD SSSDSDSDSS DSDSDSSSSD 130 140 150 160 170 180 SSSSDSDVPK KKPISKIPNK PSGTVSKTSK NSPKTTTTTT TTTTTVKSKP APKVKPEQSS 190 200 210 220 230 240 SDDSSSDSSD DSSDDSSSDS SSEEEKPKKK PSKKPAAVKK EITVKKETTT TTKKTPVKKE 250 260 270 280 290 300 VEVKKETKTT TTKKVKKEES DDDGEDEKTT TKKKTTTRKR KLKEEEEGEE EEEEGVNKWW 310 320 330 340 350 360 DKEDDEDDGT KWTTLIHNGP VFPPAYVPHG IKFMYDGKVV KLTPKQEEVA TFYANYLETD 370 380 390 400 410 420 HVKKQAFKDN FFKEFKGLLT SEQKEIVKKM DKCDFSHIHT HLKTKKEQRK ARSKEEKDAE 430 440 450 460 470 480 TAEKKKIQEK HGFATIDGFK EKVGNYMIEP PGLFLGRGQH PKTGMLKQRI MPSDVTLNIG 490 500 510 520 530 540 EGEVIPPSPI PGEKWKEIVH NNTVTWLAFW RESVNGGFKY VWLAPSSKIK GQADRKKFEV 550 560 570 580 590 600 ARGLKNCIGD IRKGYQKSFN DESTEKRQLA VALYLIDFLA LRVGNEKGED QADTVGCCSL 610 620 630 640 650 660 RVEHIKLESN NTITLDFLGK DSMRYLNTVQ IREDAYKVLK TFVKGKKPTD LLFDSLTVTQ 670 680 690 700 710 720 LNNHLKKQMT GLSAKVFRTY NASITLQKEL DKMDTKEFQS IDEKILFYNR CNREVAILCN 730 740 750 760 770 780 HQKAPPKNLA ETMSKIDEKI QELRDLQDLC RIKIGKTPKS QQEDIESREA ERLPKLIQLA 790 800 810 820 830 840 ITNKKDKDKE KTDKEISFDV KAAFEKSRTL PDAKGKIKEK IAKYEEQIKK QEILKTGKDE 850 860 870 880 890 LKTVALGTSK INYLDPRITV AWCKKNKVPV DKIFTKSLRD KFPWSDVGTD YIF

References

[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: 15875012] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: AX4.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AAFI02000051 Genomic DNA. Translation: EAL65841.1.
RefSeq	XP_639222.1. XM_634130.1.
3D structure databases
HSSP	HSSP built from PDB template 1R49 based on UniProtKB P11387.
ProteinModelPortal	Q54RC3.
SMR	Q54RC3. Positions 847-885.
ModBase	Search...
Protein-protein interaction databases
STRING	Q54RC3.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblProtists	DDB0234191; DDB0234191; DDB_G0283205.
GeneID	8623995.
GenomeReviews	Gene locus top1 in contig CM000153_GR.
KEGG	ddi:DDB_G0283205.
Organism-specific databases
dictyBase	DDB_G0283205. top1.
Phylogenomic databases
eggNOG	KOG0981.
GeneTree	EPrGT00050000000497.
HOGENOM	HBG521929.
OMA	IKEFSKC.
PhylomeDB	Q54RC3.
Family and domain databases
InterPro	IPR011010. DNA_brk_join_enz. IPR013034. DNA_topo_domain1. IPR018521. TopoI_AS. IPR001631. TopoI_C. IPR013499. TopoI_C_euk. 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. [Graphical view]
Gene3D	G3DSA:3.90.15.10. TopoI_cat_a-hlx-sub_euk. 1 hit. G3DSA:1.10.132.10. TopoI_cat_a/b-sub_euk. 2 hits. G3DSA:1.10.10.41. TopoI_DNA-bd_a-hlx_euk. 1 hit. G3DSA:2.170.11.10. TopoI_DNA-bd_mixed-a/b_euk. 2 hits.
KO	K03163.
Pfam	PF01028. Topoisom_I. 1 hit. PF02919. Topoisom_I_N. 1 hit. [Graphical view]
PRINTS	PR00416. EUTPISMRASEI.
SMART	SM00435. TOPEUc. 1 hit. [Graphical view]
SUPFAM	SSF56349. DNA_brk_join_enz. 1 hit. SSF56741. TopoI_DNA_bd_euk. 1 hit.
PROSITE	PS00176. TOPOISOMERASE_I_EUK. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

TOP1_DICDI

Accession

Primary (citable) accession number: Q54RC3

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 29, 2008
Last sequence update:	May 24, 2005
Last modified:	November 16, 2011
This is version 47 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)