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P46799

- TOP1_THEMA

UniProt

P46799 - TOP1_THEMA

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Protein

DNA topoisomerase 1

Gene

topA

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.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.UniRule annotation

Sites

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

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri559 – 58022C4-typeAdd
BLAST

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
  2. DNA topoisomerase type I activity Source: UniProtKB-HAMAP
  3. 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 1UniRule annotation (EC:5.99.1.2UniRule annotation)
Alternative name(s):
DNA topoisomerase IUniRule annotation
Omega-protein
Relaxing enzyme
Swivelase
Untwisting enzyme
Gene namesi
Name:topAUniRule annotation
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 1PRO_0000145169Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Disulfide bond

Interactioni

Subunit structurei

Monomer.UniRule annotation

Protein-protein interaction databases

STRINGi243274.TM0258.

Structurei

Secondary structure

1
633
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi8 – 125Combined sources
Helixi14 – 2411Combined sources
Helixi25 – 273Combined sources
Beta strandi28 – 325Combined sources
Beta strandi37 – 404Combined sources
Beta strandi42 – 443Combined sources
Beta strandi51 – 555Combined sources
Helixi64 – 7613Combined sources
Beta strandi79 – 813Combined sources
Helixi87 – 9913Combined sources
Helixi116 – 1249Combined sources
Helixi131 – 15929Combined sources
Helixi166 – 18520Combined sources
Beta strandi190 – 1989Combined sources
Beta strandi201 – 2055Combined sources
Helixi215 – 2228Combined sources
Beta strandi227 – 23913Combined sources
Helixi247 – 25812Combined sources
Helixi262 – 27413Combined sources
Beta strandi279 – 2835Combined sources
Helixi298 – 31114Combined sources
Helixi314 – 3163Combined sources
Helixi346 – 3494Combined sources
Turni350 – 3523Combined sources
Helixi355 – 37117Combined sources
Beta strandi376 – 38611Combined sources
Beta strandi393 – 40311Combined sources
Helixi405 – 4084Combined sources
Beta strandi431 – 4388Combined sources
Helixi447 – 45610Combined sources
Turni462 – 4643Combined sources
Helixi465 – 47410Combined sources
Beta strandi477 – 4815Combined sources
Beta strandi484 – 4885Combined sources
Helixi489 – 50113Combined sources
Turni503 – 5064Combined sources
Helixi508 – 52215Combined sources
Helixi528 – 54013Combined sources
Beta strandi553 – 5586Combined sources
Beta strandi560 – 5623Combined sources
Beta strandi564 – 5707Combined sources
Beta strandi573 – 5775Combined sources
Beta strandi579 – 5813Combined sources
Beta strandi593 – 5953Combined sources
Beta strandi598 – 6003Combined sources

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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP46799.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini6 – 115110ToprimUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni164 – 1696Interaction with DNAUniRule annotation

Sequence similaritiesi

Belongs to the type IA topoisomerase family.UniRule annotation
Contains 1 Toprim domain.UniRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri559 – 58022C4-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiCOG0551.
InParanoidiP46799.
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_dom.
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

        10         20         30         40         50
MSKKVKKYIV VESPAKAKTI KSILGNEYEV FASMGHIIDL PKSKFGVDLE
60 70 80 90 100
KDFEPEFAVI KGKEKVVEKL KDLAKKGELL IASDMDREGE AIAWHIARVT
110 120 130 140 150
NTLGRKNRIV FSEITPRVIR EAVKNPREID MKKVRAQLAR RILDRIVGYS
160 170 180 190 200
LSPVLWRNFK SNLSAGRVQS ATLKLVCDRE REILRFVPKK YHRITVNFDG
210 220 230 240 250
LTAEIDVKEK KFFDAETLKE IQSIDELVVE EKKVSVKKFA PPEPFKTSTL
260 270 280 290 300
QQEAYSKLGF SVSKTMMIAQ QLYEGVETKD GHIAFITYMR TDSTRVSDYA
310 320 330 340 350
KEEARNLITE VFGEEYVGSK RERRKSNAKI QDAHEAIRPT NVFMTPEEAG
360 370 380 390 400
KYLNSDQKKL YELIWKRFLA SQMKPSQYEE TRFVLRTKDG KYRFKGTVLK
410 420 430 440 450
KIFDGYEKVW KTERNTGEFP FEEGESVKPV VVKIEEQETK PKPRYTEGSL
460 470 480 490 500
VKEMERLGIG RPSTYASTIK LLLNRGYIKK IRGYLYPTIV GSVVMDYLEK
510 520 530 540 550
KYSDVVSVSF TAEMEKDLDE VEQGKKTDKI VLREFYESFS SVFDRNDRIV
560 570 580 590 600
VDFPTNQKCS CGKEMRLSFG KYGFYLKCEC GKTRSVKNDE IAVIDDGKIF
610 620 630
LGRKDSESGS PDGRSVEGKG NLSEKRRKGK KGS
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.
GeneIDi18092541.
897168.
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 18092541.
897168.
KEGGi tma:TM0258.
tmi:THEMA_03435.
tmm:Tmari_0256.
PATRICi 23935393. VBITheMar51294_0262.

Phylogenomic databases

eggNOGi COG0551.
InParanoidi P46799.
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_dom.
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: October 29, 2014
This is version 121 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