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Q6IM78

- TOP1M_RAT

UniProt

Q6IM78 - TOP1M_RAT

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Protein

DNA topoisomerase I, mitochondrial

Gene

Top1mt

Organism
Rattus norvegicus (Rat)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at transcript leveli

Functioni

Releases the supercoiling and torsional tension of DNA introduced during duplication of mitochondrial DNA 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.

Cofactori

Ca2+By similarity, Mg2+By similarityNote: Divalent metal ions (calcium or magnesium).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei145 – 1451Interaction with DNABy similarity
Sitei193 – 1931Interaction with DNABy similarity
Sitei241 – 2411Interaction with DNABy similarity
Sitei272 – 2721Interaction with DNABy similarity
Sitei330 – 3301Interaction with DNABy similarity
Sitei361 – 3611Interaction with DNABy similarity
Sitei403 – 4031Interaction with DNABy similarity
Sitei461 – 4611Interaction with DNABy similarity
Sitei479 – 4791Interaction with DNABy similarity
Active sitei551 – 5511O-(3'-phospho-DNA)-tyrosine intermediateBy similarity

GO - Molecular functioni

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

GO - Biological processi

  1. DNA replication Source: RefGenome
  2. DNA topological change Source: RefGenome
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase I, mitochondrial (EC:5.99.1.2)
Short name:
TOP1mt
Gene namesi
Name:Top1mt
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
ProteomesiUP000002494: Chromosome 7

Organism-specific databases

RGDi1303177. Top1mt.

Subcellular locationi

Mitochondrion By similarity

GO - Cellular componenti

  1. chromosome Source: InterPro
  2. mitochondrial nucleoid Source: RefGenome
  3. nucleus Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 4343MitochondrionBy similarityAdd
BLAST
Chaini44 – 593550DNA topoisomerase I, mitochondrialPRO_0000384395Add
BLAST

Proteomic databases

PaxDbiQ6IM78.
PRIDEiQ6IM78.

Expressioni

Gene expression databases

GenevestigatoriQ6IM78.

Interactioni

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000009965.

Structurei

3D structure databases

ProteinModelPortaliQ6IM78.
SMRiQ6IM78. Positions 38-593.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni254 – 2552Interaction with DNABy similarity
Regioni317 – 3226Interaction with DNABy similarity
Regioni414 – 4163Interaction with DNABy similarity

Sequence similaritiesi

Belongs to the type IB topoisomerase family.Curated

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG3569.
GeneTreeiENSGT00390000016347.
HOGENOMiHOG000105469.
InParanoidiQ6IM78.
KOiK03163.
OMAiVINCSRD.
OrthoDBiEOG7CVPX5.
PhylomeDBiQ6IM78.
TreeFamiTF105281.

Family and domain databases

Gene3Di1.10.10.41. 1 hit.
1.10.132.10. 1 hit.
2.170.11.10. 2 hits.
3.90.15.10. 1 hit.
InterProiIPR011010. DNA_brk_join_enz.
IPR013034. DNA_topo_domain1.
IPR001631. TopoI.
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.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q6IM78-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MLLLWLRALC RRFQHVPRRV PSRQVSRGSK ASRAGWGETS KSSVKWKQLE
60 70 80 90 100
HKGPCFAPAY EPLPDGVRFF YDGKPVRLSL AAEEVATFYG KMLHLECTTK
110 120 130 140 150
EVFRRNFFSD WQKEMTAEER KLITHLDKCD FSEIHRHFME RAEARRTLPR
160 170 180 190 200
EQKQKLKEEA EKLQQEFGYC ILDGHREKIG NFKTEPPGLF RGRGDHPKMG
210 220 230 240 250
MLKRRVMPED VVINCSRDSK IPEPPAGHQW KEVRSDNTVM WLAAWVENIQ
260 270 280 290 300
NSFKYIILNP SSKPKGEMDW QKYEVARRLK GVVDKIRAQY QADWKSPEMK
310 320 330 340 350
KRQLAVALYF IDKLALRTGN EKEEGETADT VGCCSLRVEH VRLHTPADGQ
360 370 380 390 400
EHVVELDFLG KDSIRYKNHV TVEKLVFQNL QHFMEDKDPR DDLFDALTTS
410 420 430 440 450
SLNKHLQDLM EGLTAKVFRT YNASITLQEQ LRVLTRAEDS LTCKVLAYNR
460 470 480 490 500
ANRAVAVLCN HQRAIPKTFE ESMQTLQKKI ETKKAQVAEA QVELQKAETD
510 520 530 540 550
LRMRGDSKSK SFLQKQQRLL KLEEQLARLC TKATDKEENK QVALGTAKLN
560 570 580 590
YLDPRISIAW CKRFGVPVEK IYNKTQRERF AWAFNQAGED FEF
Length:593
Mass (Da):69,011
Last modified:July 5, 2004 - v1
Checksum:i6B691D668970BD9E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BK001786 mRNA. Translation: DAA02296.1.
RefSeqiNP_001002798.1. NM_001002798.1.
UniGeneiRn.31307.

Genome annotation databases

EnsembliENSRNOT00000009965; ENSRNOP00000009965; ENSRNOG00000007500.
GeneIDi300029.
KEGGirno:300029.
UCSCiRGD:1303177. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BK001786 mRNA. Translation: DAA02296.1 .
RefSeqi NP_001002798.1. NM_001002798.1.
UniGenei Rn.31307.

3D structure databases

ProteinModelPortali Q6IM78.
SMRi Q6IM78. Positions 38-593.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 10116.ENSRNOP00000009965.

Proteomic databases

PaxDbi Q6IM78.
PRIDEi Q6IM78.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSRNOT00000009965 ; ENSRNOP00000009965 ; ENSRNOG00000007500 .
GeneIDi 300029.
KEGGi rno:300029.
UCSCi RGD:1303177. rat.

Organism-specific databases

CTDi 116447.
RGDi 1303177. Top1mt.

Phylogenomic databases

eggNOGi COG3569.
GeneTreei ENSGT00390000016347.
HOGENOMi HOG000105469.
InParanoidi Q6IM78.
KOi K03163.
OMAi VINCSRD.
OrthoDBi EOG7CVPX5.
PhylomeDBi Q6IM78.
TreeFami TF105281.

Miscellaneous databases

NextBioi 646149.
PROi Q6IM78.

Gene expression databases

Genevestigatori Q6IM78.

Family and domain databases

Gene3Di 1.10.10.41. 1 hit.
1.10.132.10. 1 hit.
2.170.11.10. 2 hits.
3.90.15.10. 1 hit.
InterProi IPR011010. DNA_brk_join_enz.
IPR013034. DNA_topo_domain1.
IPR001631. TopoI.
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.
ProtoNeti Search...

Publicationsi

  1. "Thirteen-exon-motif signature for vertebrate nuclear and mitochondrial type IB topoisomerases."
    Zhang H., Meng L.-H., Zimonjic D.B., Popescu N.C., Pommier Y.
    Nucleic Acids Res. 32:2087-2092(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].

Entry informationi

Entry nameiTOP1M_RAT
AccessioniPrimary (citable) accession number: Q6IM78
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 22, 2009
Last sequence update: July 5, 2004
Last modified: November 26, 2014
This is version 80 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3