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P46799

- TOP1_THEMA

UniProt

P46799 - TOP1_THEMA

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Protein
DNA topoisomerase 1
Gene
topA, TM_0258
Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Status
Reviewed - Annotation score: 4 out of 5 - Experimental evidence at protein leveli

Functioni

Releases the supercoiling and torsional tension of DNA, which is 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-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-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 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone By similarity.UniRule annotation

Catalytic activityi

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.UniRule annotation

Cofactori

Magnesium. Binds two Mg2+ per subunit By similarity.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi12 – 121Magnesium 1; catalytic By similarity
Sitei36 – 361Interaction with DNA By similarity
Metal bindingi84 – 841Magnesium 1; catalytic By similarity
Metal bindingi84 – 841Magnesium 2 By similarity
Metal bindingi86 – 861Magnesium 2 By similarity
Sitei140 – 1401Interaction with DNA By similarity
Sitei141 – 1411Interaction with DNA By similarity
Sitei144 – 1441Interaction with DNA By similarity
Sitei149 – 1491Interaction with DNA By similarity
Sitei156 – 1561Interaction with DNA By similarity
Active sitei288 – 2881O-(5'-phospho-DNA)-tyrosine intermediate By similarity
Sitei290 – 2901Interaction with DNA By similarity
Sitei475 – 4751Interaction with DNA By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri559 – 58022C4-typeUniRule annotation
Add
BLAST

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. DNA binding Source: UniProtKB-KW
  3. DNA topoisomerase type I activity Source: UniProtKB-HAMAP
  4. magnesium ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. DNA topological change Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 1 (EC:5.99.1.2)
Alternative name(s):
DNA topoisomerase I
Omega-protein
Relaxing enzyme
Swivelase
Untwisting enzyme
Gene namesi
Name:topA
Ordered Locus Names:TM_0258
OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Taxonomic identifieri243274 [NCBI]
Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
ProteomesiUP000008183: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 633633DNA topoisomerase 1UniRule annotation
PRO_0000145169Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi559 ↔ 578UniRule annotation
Disulfide bondi561 ↔ 580UniRule annotation

Keywords - PTMi

Disulfide bond

Interactioni

Subunit structurei

Monomer By similarity.UniRule annotation

Protein-protein interaction databases

STRINGi243274.TM0258.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi8 – 125
Helixi14 – 2411
Helixi25 – 273
Beta strandi28 – 325
Beta strandi37 – 404
Beta strandi42 – 443
Beta strandi51 – 555
Helixi64 – 7613
Beta strandi79 – 813
Helixi87 – 9913
Helixi116 – 1249
Helixi131 – 15929
Helixi166 – 18520
Beta strandi190 – 1989
Beta strandi201 – 2055
Helixi215 – 2228
Beta strandi227 – 23913
Helixi247 – 25812
Helixi262 – 27413
Beta strandi279 – 2835
Helixi298 – 31114
Helixi314 – 3163
Helixi346 – 3494
Turni350 – 3523
Helixi355 – 37117
Beta strandi376 – 38611
Beta strandi393 – 40311
Helixi405 – 4084
Beta strandi431 – 4388
Helixi447 – 45610
Turni462 – 4643
Helixi465 – 47410
Beta strandi477 – 4815
Beta strandi484 – 4885
Helixi489 – 50113
Turni503 – 5064
Helixi508 – 52215
Helixi528 – 54013
Beta strandi553 – 5586
Beta strandi560 – 5623
Beta strandi564 – 5707
Beta strandi573 – 5775
Beta strandi579 – 5813
Beta strandi593 – 5953
Beta strandi598 – 6003

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2GAIX-ray1.70A/B3-633[»]
2GAJX-ray1.95A/B3-633[»]
ProteinModelPortaliP46799.
SMRiP46799. Positions 7-601.

Miscellaneous databases

EvolutionaryTraceiP46799.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini6 – 115110Toprim
Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni164 – 1696Interaction with DNA By similarity

Sequence similaritiesi

Contains 1 Toprim domain.

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG0551.
KOiK03168.
OMAiWINKAKK.
OrthoDBiEOG6S7XQ9.

Family and domain databases

Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00952. Topoisom_1_prok.
InterProiIPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR023406. Topo_IA_AS.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013825. Topo_IA_cen_sub2.
IPR023405. Topo_IA_core_domain.
IPR003602. Topo_IA_DNA-bd.
IPR005733. TopoI_bac-type.
IPR028612. Topoisom_1_IA.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 1 hit.
TIGRFAMsiTIGR01051. topA_bact. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P46799-1 [UniParc]FASTAAdd to Basket

« Hide

MSKKVKKYIV VESPAKAKTI KSILGNEYEV FASMGHIIDL PKSKFGVDLE    50
KDFEPEFAVI KGKEKVVEKL KDLAKKGELL IASDMDREGE AIAWHIARVT 100
NTLGRKNRIV FSEITPRVIR EAVKNPREID MKKVRAQLAR RILDRIVGYS 150
LSPVLWRNFK SNLSAGRVQS ATLKLVCDRE REILRFVPKK YHRITVNFDG 200
LTAEIDVKEK KFFDAETLKE IQSIDELVVE EKKVSVKKFA PPEPFKTSTL 250
QQEAYSKLGF SVSKTMMIAQ QLYEGVETKD GHIAFITYMR TDSTRVSDYA 300
KEEARNLITE VFGEEYVGSK RERRKSNAKI QDAHEAIRPT NVFMTPEEAG 350
KYLNSDQKKL YELIWKRFLA SQMKPSQYEE TRFVLRTKDG KYRFKGTVLK 400
KIFDGYEKVW KTERNTGEFP FEEGESVKPV VVKIEEQETK PKPRYTEGSL 450
VKEMERLGIG RPSTYASTIK LLLNRGYIKK IRGYLYPTIV GSVVMDYLEK 500
KYSDVVSVSF TAEMEKDLDE VEQGKKTDKI VLREFYESFS SVFDRNDRIV 550
VDFPTNQKCS CGKEMRLSFG KYGFYLKCEC GKTRSVKNDE IAVIDDGKIF 600
LGRKDSESGS PDGRSVEGKG NLSEKRRKGK KGS 633
Length:633
Mass (Da):72,695
Last modified:November 1, 1995 - v1
Checksum:iF7262A044060CFE9
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U27841 Genomic DNA. Translation: AAA68949.1.
AE000512 Genomic DNA. Translation: AAD35346.1.
PIRiS62737.
RefSeqiNP_228071.1. NC_000853.1.
YP_007976607.1. NC_021214.1.
YP_008990768.1. NC_023151.1.

Genome annotation databases

EnsemblBacteriaiAAD35346; AAD35346; TM_0258.
GeneIDi897168.
KEGGitma:TM0258.
tmi:THEMA_03435.
tmm:Tmari_0256.
PATRICi23935393. VBITheMar51294_0262.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
U27841 Genomic DNA. Translation: AAA68949.1 .
AE000512 Genomic DNA. Translation: AAD35346.1 .
PIRi S62737.
RefSeqi NP_228071.1. NC_000853.1.
YP_007976607.1. NC_021214.1.
YP_008990768.1. NC_023151.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2GAI X-ray 1.70 A/B 3-633 [» ]
2GAJ X-ray 1.95 A/B 3-633 [» ]
ProteinModelPortali P46799.
SMRi P46799. Positions 7-601.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 243274.TM0258.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAD35346 ; AAD35346 ; TM_0258 .
GeneIDi 897168.
KEGGi tma:TM0258.
tmi:THEMA_03435.
tmm:Tmari_0256.
PATRICi 23935393. VBITheMar51294_0262.

Phylogenomic databases

eggNOGi COG0551.
KOi K03168.
OMAi WINKAKK.
OrthoDBi EOG6S7XQ9.

Miscellaneous databases

EvolutionaryTracei P46799.

Family and domain databases

Gene3Di 1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPi MF_00952. Topoisom_1_prok.
InterProi IPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR023406. Topo_IA_AS.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013825. Topo_IA_cen_sub2.
IPR023405. Topo_IA_core_domain.
IPR003602. Topo_IA_DNA-bd.
IPR005733. TopoI_bac-type.
IPR028612. Topoisom_1_IA.
IPR006171. Toprim_domain.
[Graphical view ]
PANTHERi PTHR11390. PTHR11390. 1 hit.
Pfami PF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view ]
PRINTSi PR00417. PRTPISMRASEI.
SMARTi SM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view ]
SUPFAMi SSF56712. SSF56712. 1 hit.
TIGRFAMsi TIGR01051. topA_bact. 1 hit.
PROSITEi PS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and sequencing of the gene coding for topoisomerase I from the extremely thermophilic eubacterium, Thermotoga maritima."
    Bouthier de la Tour C., Kaltoum H., Portemer C., Confalonieri F., Huber R., Duguet M.
    Biochim. Biophys. Acta 1264:279-283(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
  3. "Crystal structure of full length topoisomerase I from Thermotoga maritima."
    Hansen G., Harrenga A., Wieland B., Schomburg D., Reinemer P.
    J. Mol. Biol. 358:1328-1340(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 3-633.

Entry informationi

Entry nameiTOP1_THEMA
AccessioniPrimary (citable) accession number: P46799
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: September 3, 2014
This is version 119 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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