Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

DNA topoisomerase 1

Gene

topA

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Status
Reviewed-Annotation score: 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

Mg2+UniRule annotationNote: Binds two Mg2+ per subunit.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi12Magnesium 1; catalyticUniRule annotation1
Metal bindingi84Magnesium 1; catalyticUniRule annotation1
Metal bindingi84Magnesium 2UniRule annotation1
Metal bindingi86Magnesium 2UniRule annotation1
Active sitei288O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri559 – 580C4-typeAdd BLAST22

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

BRENDAi5.99.1.2. 6331.

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
Proteomesi
  • UP000008183 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001451691 – 633DNA topoisomerase 1Add BLAST633

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Disulfide bondi559 ↔ 5781 Publication
Disulfide bondi561 ↔ 5801 Publication

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiP46799.

Interactioni

Subunit structurei

Monomer.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei36Interaction with DNAUniRule annotation1
Sitei140Interaction with DNAUniRule annotation1
Sitei141Interaction with DNAUniRule annotation1
Sitei144Interaction with DNAUniRule annotation1
Sitei149Interaction with DNAUniRule annotation1
Sitei156Interaction with DNAUniRule annotation1
Sitei290Interaction with DNAUniRule annotation1
Sitei475Interaction with DNAUniRule annotation1

Protein-protein interaction databases

STRINGi243274.TM0258.

Structurei

Secondary structure

1633
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi8 – 12Combined sources5
Helixi14 – 24Combined sources11
Helixi25 – 27Combined sources3
Beta strandi28 – 32Combined sources5
Beta strandi37 – 40Combined sources4
Beta strandi42 – 44Combined sources3
Beta strandi51 – 55Combined sources5
Helixi64 – 76Combined sources13
Beta strandi79 – 81Combined sources3
Helixi87 – 99Combined sources13
Helixi116 – 124Combined sources9
Helixi131 – 159Combined sources29
Helixi166 – 185Combined sources20
Beta strandi190 – 198Combined sources9
Beta strandi201 – 205Combined sources5
Helixi215 – 222Combined sources8
Beta strandi227 – 239Combined sources13
Helixi247 – 258Combined sources12
Helixi262 – 274Combined sources13
Beta strandi279 – 283Combined sources5
Helixi298 – 311Combined sources14
Helixi314 – 316Combined sources3
Helixi346 – 349Combined sources4
Turni350 – 352Combined sources3
Helixi355 – 371Combined sources17
Beta strandi376 – 386Combined sources11
Beta strandi393 – 403Combined sources11
Helixi405 – 408Combined sources4
Beta strandi431 – 438Combined sources8
Helixi447 – 456Combined sources10
Turni462 – 464Combined sources3
Helixi465 – 474Combined sources10
Beta strandi477 – 481Combined sources5
Beta strandi484 – 488Combined sources5
Helixi489 – 501Combined sources13
Turni503 – 506Combined sources4
Helixi508 – 522Combined sources15
Helixi528 – 540Combined sources13
Beta strandi553 – 558Combined sources6
Beta strandi560 – 562Combined sources3
Beta strandi564 – 570Combined sources7
Beta strandi573 – 577Combined sources5
Beta strandi579 – 581Combined sources3
Beta strandi593 – 595Combined sources3
Beta strandi598 – 600Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2GAIX-ray1.70A/B3-633[»]
2GAJX-ray1.95A/B3-633[»]
ProteinModelPortaliP46799.
SMRiP46799.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP46799.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini6 – 115ToprimUniRule annotationAdd BLAST110

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni164 – 169Interaction with DNAUniRule annotation6

Sequence similaritiesi

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

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri559 – 580C4-typeAdd BLAST22

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiENOG4105C73. Bacteria.
COG0550. LUCA.
COG0551. LUCA.
InParanoidiP46799.
KOiK03168.
OMAiYNWVIDY.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00952. Topoisom_1_prok. 1 hit.
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:
EMBLi
GenBanki
DDBJi
Links Updated
U27841 Genomic DNA. Translation: AAA68949.1.
AE000512 Genomic DNA. Translation: AAD35346.1.
PIRiS62737.
RefSeqiNP_228071.1. NC_000853.1.
WP_004082962.1. NZ_CP011107.1.

Genome annotation databases

EnsemblBacteriaiAAD35346; AAD35346; TM_0258.
GeneIDi897168.
KEGGitma:TM0258.
PATRICi23935393. VBITheMar51294_0262.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U27841 Genomic DNA. Translation: AAA68949.1.
AE000512 Genomic DNA. Translation: AAD35346.1.
PIRiS62737.
RefSeqiNP_228071.1. NC_000853.1.
WP_004082962.1. NZ_CP011107.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2GAIX-ray1.70A/B3-633[»]
2GAJX-ray1.95A/B3-633[»]
ProteinModelPortaliP46799.
SMRiP46799.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243274.TM0258.

Proteomic databases

PRIDEiP46799.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD35346; AAD35346; TM_0258.
GeneIDi897168.
KEGGitma:TM0258.
PATRICi23935393. VBITheMar51294_0262.

Phylogenomic databases

eggNOGiENOG4105C73. Bacteria.
COG0550. LUCA.
COG0551. LUCA.
InParanoidiP46799.
KOiK03168.
OMAiYNWVIDY.

Enzyme and pathway databases

BRENDAi5.99.1.2. 6331.

Miscellaneous databases

EvolutionaryTraceiP46799.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00952. Topoisom_1_prok. 1 hit.
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]
ProtoNetiSearch...

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: November 2, 2016
This is version 137 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

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 one 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.