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Protein

DNA topoisomerase 1

Gene

topA

Organism
Methylocella silvestris (strain DSM 15510 / CIP 108128 / LMG 27833 / NCIMB 13906 / BL2)
Status
Unreviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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 annotationSAAS annotation

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi7Magnesium 1; catalyticUniRule annotation1
Metal bindingi80Magnesium 1; catalyticUniRule annotation1
Metal bindingi80Magnesium 2UniRule annotation1
Metal bindingi82Magnesium 2UniRule annotation1
Active sitei303O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, TopoisomeraseUniRule annotationSAAS annotation

Keywords - Ligandi

DNA-bindingUniRule annotationSAAS annotation, MagnesiumUniRule annotationSAAS annotation, Metal-bindingUniRule annotationSAAS annotation

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 1UniRule annotation (EC:5.99.1.2UniRule annotation)
Alternative name(s):
DNA topoisomerase IUniRule annotation
Gene namesi
Name:topAUniRule annotation
Ordered Locus Names:Msil_3847Imported
OrganismiMethylocella silvestris (strain DSM 15510 / CIP 108128 / LMG 27833 / NCIMB 13906 / BL2)Imported
Taxonomic identifieri395965 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBeijerinckiaceaeMethylocella
Proteomesi
  • UP000002257 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Interactioni

Subunit structurei

Monomer.UniRule annotationSAAS annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei31Interaction with DNAUniRule annotation1
Sitei141Interaction with DNAUniRule annotation1
Sitei142Interaction with DNAUniRule annotation1
Sitei145Interaction with DNAUniRule annotation1
Sitei157Interaction with DNAUniRule annotation1
Sitei305Interaction with DNAUniRule annotation1
Sitei500Interaction with DNAUniRule annotation1

Protein-protein interaction databases

STRINGi395965.Msil_3847.

Structurei

3D structure databases

ProteinModelPortaliB8EMQ0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 117ToprimInterPro annotationAdd BLAST117

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni165 – 170Interaction with DNAUniRule annotation6

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105C73. Bacteria.
COG0550. LUCA.
COG1754. LUCA.
HOGENOMiHOG000004020.
KOiK03168.
OMAiFRSAEYW.
OrthoDBiPOG091H02BN.

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.
IPR013498. Topo_IA_Znf.
IPR005733. TopoI_bac-type.
IPR028612. Topoisom_1_IA.
IPR025589. Toprim_C_rpt.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF13368. Toprim_C_rpt. 4 hits.
PF01396. zf-C4_Topoisom. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 2 hits.
TIGRFAMsiTIGR01051. topA_bact. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

B8EMQ0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYVVIVESPA KAKSINKYLG KGYEVYPSYG HVRDLPAKDG SVDPDADFAM
60 70 80 90 100
LWDVDVKSAK RLNEIARAVK DADKIILATD PDREGEAISW HVLEVLKAKK
110 120 130 140 150
VLKDKPVERV VFNAITKSAV LEAMQHPRQI DVALVDAYLA RRALDYLVGF
160 170 180 190 200
NLSPVLWRKL PGARSAGRVQ SVALRLVCDR ELEIEAFVAR EYWSIVAHLR
210 220 230 240 250
TQADAPFTAR LVGADGKKIT RLDVGTGAEA AAFKTDLENA TFRVAEIEAK
260 270 280 290 300
PAKRHPSAPF TTSTLQQEAS RKLGFAPART MQLAQRLYEG ADIDGETVGL
310 320 330 340 350
ITYMRTDGVD LAPEAITSAR SVIARQFGDA YVPKAPRKYT VKAKNAQEAH
360 370 380 390 400
EAIRPTDLAR LPRAVARALE PDQAKLYELI WTRTIASQME SAELERTTVD
410 420 430 440 450
IEALAGARKL DLRATGQVVR FDGFLKLYQE GRDDEDDDES ARLPDMAKDE
460 470 480 490 500
RLKRERIEAD QHFTEPPPRF TEATLVKRME ELGIGRPSTY ASTLAVLRER
510 520 530 540 550
DYVRIEKKRL HPEDKGRLVT AFLEAFFARY VGYDFTADLE EKLDRVSNHE
560 570 580 590 600
IDWKQVLRDF WLDFSGALAG TKDLRTTEVL DRLNEILGPH IFPPKEDGSD
610 620 630 640 650
PRGCPSCGEG KLSLKLGKFG AFIGCSNYPE CKFTRTLAAP DGAEANGGER
660 670 680 690 700
PGVKSLGVDP DSGEEITLRD GRFGVYVQQG EGEKPKRSSL PPTIAPADLT
710 720 730 740 750
LEQAIALLSL PREVARHPES KEPIVAGIGR YGPYVQHGKT YANVAKDEDI
760 770 780 790 800
ISIGANRAID LIVAKESGLT GRRFGASESA PARVLGEHPA GGAVSVKAGR
810 820 830 840 850
YGPYVTHGKI NATLPKEADP TTLTLEGAVA LLAAKASGGG APMQGRLLGD
860 870 880 890 900
HPSGGPITVR AGRFGAYVNH GKTNATLKRD ASAETITLEE AIRLIEDKEA
910 920 930 940 950
AGGGPRKAAA PKKAAKSSAA AKKAAPNAKN KTAPANDEDP PFEPSPNRKP
960 970
AAKAAAAAHK KPAAKAAAAK LKQAKQA
Length:977
Mass (Da):106,066
Last modified:March 3, 2009 - v1
Checksum:iD99B73E5B0748473
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001280 Genomic DNA. Translation: ACK52729.1.
RefSeqiWP_012592797.1. NC_011666.1.

Genome annotation databases

EnsemblBacteriaiACK52729; ACK52729; Msil_3847.
KEGGimsl:Msil_3847.
PATRICi22603546. VBIMetSil55537_4120.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001280 Genomic DNA. Translation: ACK52729.1.
RefSeqiWP_012592797.1. NC_011666.1.

3D structure databases

ProteinModelPortaliB8EMQ0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi395965.Msil_3847.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACK52729; ACK52729; Msil_3847.
KEGGimsl:Msil_3847.
PATRICi22603546. VBIMetSil55537_4120.

Phylogenomic databases

eggNOGiENOG4105C73. Bacteria.
COG0550. LUCA.
COG1754. LUCA.
HOGENOMiHOG000004020.
KOiK03168.
OMAiFRSAEYW.
OrthoDBiPOG091H02BN.

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.
IPR013498. Topo_IA_Znf.
IPR005733. TopoI_bac-type.
IPR028612. Topoisom_1_IA.
IPR025589. Toprim_C_rpt.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF13368. Toprim_C_rpt. 4 hits.
PF01396. zf-C4_Topoisom. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 2 hits.
TIGRFAMsiTIGR01051. topA_bact. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiB8EMQ0_METSB
AccessioniPrimary (citable) accession number: B8EMQ0
Entry historyi
Integrated into UniProtKB/TrEMBL: March 3, 2009
Last sequence update: March 3, 2009
Last modified: November 2, 2016
This is version 66 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteomeImported

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.