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Protein

DNA topoisomerase 1

Gene

TOP1

Organism
Ustilago maydis (strain 521 / FGSC 9021) (Corn smut fungus)
Status
Reviewed-Annotation score: Annotation score: 4 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
Sitei317 – 3171Interaction with DNABy similarity
Sitei366 – 3661Interaction with DNABy similarity
Sitei397 – 3971Interaction with DNABy similarity
Sitei454 – 4541Interaction with DNABy similarity
Sitei480 – 4801Interaction with DNABy similarity
Sitei545 – 5451Interaction with DNABy similarity
Sitei613 – 6131Interaction with DNABy similarity
Sitei632 – 6321Interaction with DNABy similarity
Active sitei822 – 8221O-(3'-phospho-DNA)-tyrosine intermediatePROSITE-ProRule annotation

GO - Molecular functioni

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

GO - Biological processi

  1. chromatin assembly or disassembly Source: EnsemblFungi
  2. chromatin silencing at rDNA Source: EnsemblFungi
  3. DNA strand elongation involved in DNA replication Source: EnsemblFungi
  4. DNA topological change Source: EnsemblFungi
  5. mitotic chromosome condensation Source: EnsemblFungi
  6. nuclear migration Source: EnsemblFungi
  7. regulation of mitotic recombination Source: EnsemblFungi
  8. regulation of transcription from RNA polymerase II promoter Source: EnsemblFungi
  9. transcription elongation from RNA polymerase II promoter Source: EnsemblFungi
  10. transcription of nuclear large rRNA transcript from RNA polymerase I promoter Source: EnsemblFungi
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:UM05101
OrganismiUstilago maydis (strain 521 / FGSC 9021) (Corn smut fungus)
Taxonomic identifieri237631 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaBasidiomycotaUstilaginomycotinaUstilaginomycetesUstilaginalesUstilaginaceaeUstilago

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: EnsemblFungi
  2. nucleolus Source: EnsemblFungi
  3. replication fork protection complex Source: EnsemblFungi
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10191019DNA topoisomerase 1PRO_0000145210Add
BLAST

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

STRINGi5270.UM05101.1.

Structurei

3D structure databases

SMRiP41511. Positions 812-837.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni379 – 3802Interaction with DNABy similarity
Regioni442 – 4476Interaction with DNABy similarity
Regioni556 – 5583Interaction with DNABy similarity

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi108 – 11811Poly-AspAdd
BLAST
Compositional biasi121 – 1244Poly-Asp
Compositional biasi127 – 13610Poly-Asp
Compositional biasi856 – 8594Poly-Glu

Sequence similaritiesi

Belongs to the type IB topoisomerase family.Curated

Phylogenomic databases

eggNOGiCOG3569.
InParanoidiP41511.
KOiK03163.
OrthoDBiEOG7966R0.

Family and domain databases

Gene3Di1.10.10.41. 1 hit.
1.10.132.10. 3 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.

P41511-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNSIQVKNEP MLASFASTST NGKAKRSAKP SLFSGSEVSS DDDEEKPLAK
60 70 80 90 100
RPKVEDSDSD APLTSTVSSQ NGVQKRSGSS NNDDNDDDSD SDSDAPLTAL
110 120 130 140 150
VKKSNGSDDD EDDDDDDDEG DDDDEEDDDD DDDDDDKPLS KSSKSNRKPP
160 170 180 190 200
KTMSITGSGE KKWDVLIHKG PRFPDPYQPL PKDVKLKYDG RPVDLPWQTE
210 220 230 240 250
EIAMFYAVKL ETQHAQNAIF NRNFFDDFKT DLKKYPPRDG TQIKSFDKLD
260 270 280 290 300
FRDMYNYWRS LKDAELERKK ALAPSARKRE IEERKAEETK WKICLVDGVE
310 320 330 340 350
QRVGNVNVEP PGLFLGRGAH PKAGKVKRRI SPGDITINHS ADHPAPQPPA
360 370 380 390 400
GMGDWAEVVE KKDVTWLAYW KENINGQYKY VFLDATSNFK TNSDREKFEK
410 420 430 440 450
ARKLDTVVKQ IRRDVNKNLK SKVRHERQIA TIVWLIDNFS LRAGNEKGED
460 470 480 490 500
EAETYGVCSL RCEHAQIKMP DTIHLEFLGK DSMKFEEDLK ITNPDVFKNI
510 520 530 540 550
AMFLKSNGMK DKSGNYVRKK PSDPIFCAPE SGSGKMQPLQ PNSVNQFLSK
560 570 580 590 600
YMKGLSAKVF RTYNASVTFQ GLLEQTEEWL KSRPNAAERE INQTNLRLAY
610 620 630 640 650
NEANRQVAIL CNHQKTVNPM LLNRNLERTQ DKIFQIRYEI MKEQQKILTF
660 670 680 690 700
HKVSELKKEF KVKEHPFMKQ FDKIMQKQDL DAEKVKQYEE QMISDKKSKL
710 720 730 740 750
ESTFKRQQSE LQYQLEQKGL TGDDGTPKKG KKAKNVEEEV RSSIKGFKDK
760 770 780 790 800
KQVDEELKAL NETAKRLEKE RKTNKSQATS CNFVSSAKKI LSKYEMIKKQ
810 820 830 840 850
EAELVNKNNT SDVALSTSKL NYIDPRITLA WLKEWDDRLS DLGQGKAAPK
860 870 880 890 900
KKVKKEEEEN DIKPKKKDAK GAASKKRAAK TGLANSTGDS EKMELGLQVM
910 920 930 940 950
NISQFFANAL QKKFKWAASG DDGRDISAKW VFVKDAQSKM RKLDSAERKG
960 970 980 990 1000
QKGGSMAAMT DAADSKEAQP KVNCVLKKQT SADRKMSKPI KAVDKTEESD
1010
DDLSSDSSDD EDKPLAAVV
Length:1,019
Mass (Da):115,545
Last modified:December 12, 2006 - v2
Checksum:i7E89EDE7201E7FA2
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti181 – 1811P → A in AAC37415 (PubMed:7937091).Curated
Sequence conflicti197 – 1971W → C in AAC37415 (PubMed:7937091).Curated
Sequence conflicti341 – 3411A → G in AAC37415 (PubMed:7937091).Curated
Sequence conflicti434 – 4341W → C in AAC37415 (PubMed:7937091).Curated
Sequence conflicti452 – 4521A → T in AAC37415 (PubMed:7937091).Curated
Sequence conflicti1011 – 10111E → G in AAC37415 (PubMed:7937091).Curated
Sequence conflicti1017 – 10171A → S in AAC37415 (PubMed:7937091).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L32017 Genomic DNA. Translation: AAC37415.1.
AACP01000188 Genomic DNA. Translation: EAK82975.1.
PIRiS53694.

Genome annotation databases

KEGGiuma:UM05101.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L32017 Genomic DNA. Translation: AAC37415.1.
AACP01000188 Genomic DNA. Translation: EAK82975.1.
PIRiS53694.

3D structure databases

SMRiP41511. Positions 812-837.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi5270.UM05101.1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

KEGGiuma:UM05101.1.

Phylogenomic databases

eggNOGiCOG3569.
InParanoidiP41511.
KOiK03163.
OrthoDBiEOG7966R0.

Family and domain databases

Gene3Di1.10.10.41. 1 hit.
1.10.132.10. 3 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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The topoisomerase I gene from Ustilago maydis: sequence, disruption and mutant phenotype."
    Gerhold D., Thiyagarajan M., Kmiec E.B.
    Nucleic Acids Res. 22:3773-3778(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 90884 / UCM005.
  2. "Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis."
    Kaemper J., Kahmann R., Boelker M., Ma L.-J., Brefort T., Saville B.J., Banuett F., Kronstad J.W., Gold S.E., Mueller O., Perlin M.H., Woesten H.A.B., de Vries R., Ruiz-Herrera J., Reynaga-Pena C.G., Snetselaar K., McCann M., Perez-Martin J.
    , Feldbruegge M., Basse C.W., Steinberg G., Ibeas J.I., Holloman W., Guzman P., Farman M.L., Stajich J.E., Sentandreu R., Gonzalez-Prieto J.M., Kennell J.C., Molina L., Schirawski J., Mendoza-Mendoza A., Greilinger D., Muench K., Roessel N., Scherer M., Vranes M., Ladendorf O., Vincon V., Fuchs U., Sandrock B., Meng S., Ho E.C.H., Cahill M.J., Boyce K.J., Klose J., Klosterman S.J., Deelstra H.J., Ortiz-Castellanos L., Li W., Sanchez-Alonso P., Schreier P.H., Haeuser-Hahn I., Vaupel M., Koopmann E., Friedrich G., Voss H., Schlueter T., Margolis J., Platt D., Swimmer C., Gnirke A., Chen F., Vysotskaia V., Mannhaupt G., Gueldener U., Muensterkoetter M., Haase D., Oesterheld M., Mewes H.-W., Mauceli E.W., DeCaprio D., Wade C.M., Butler J., Young S.K., Jaffe D.B., Calvo S.E., Nusbaum C., Galagan J.E., Birren B.W.
    Nature 444:97-101(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 521 / FGSC 9021.

Entry informationi

Entry nameiTOP1_USTMA
AccessioniPrimary (citable) accession number: P41511
Secondary accession number(s): Q4P462
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: December 12, 2006
Last modified: April 29, 2015
This is version 87 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.