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B8EMQ0

- B8EMQ0_METSB

UniProt

B8EMQ0 - B8EMQ0_METSB

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Protein

DNA topoisomerase 1

Gene

topA

Organism
Methylocella silvestris (strain BL2 / DSM 15510 / NCIMB 13906)
Status
Unreviewed - 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 annotationSAAS annotation

Catalytic activityi

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

Cofactori

Note: Magnesium. Binds two Mg(2+) per subunit.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi7 – 71Magnesium 1; catalyticUniRule annotation
Sitei31 – 311Interaction with DNAUniRule annotation
Metal bindingi80 – 801Magnesium 1; catalyticUniRule annotation
Metal bindingi80 – 801Magnesium 2UniRule annotation
Metal bindingi82 – 821Magnesium 2UniRule annotation
Sitei141 – 1411Interaction with DNAUniRule annotation
Sitei142 – 1421Interaction with DNAUniRule annotation
Sitei145 – 1451Interaction with DNAUniRule annotation
Sitei157 – 1571Interaction with DNAUniRule annotation
Active sitei303 – 3031O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation
Sitei305 – 3051Interaction with DNAUniRule annotation
Sitei500 – 5001Interaction with DNAUniRule annotation

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, TopoisomeraseUniRule annotation

Keywords - Ligandi

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

Enzyme and pathway databases

BioCyciMSIL395965:GCND-3902-MONOMER.

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 BL2 / DSM 15510 / NCIMB 13906)Imported
Taxonomic identifieri395965 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBeijerinckiaceaeMethylocella
ProteomesiUP000002257: Chromosome

Subcellular locationi

GO - Cellular componenti

  1. chromosome Source: InterPro
Complete GO annotation...

Interactioni

Subunit structurei

Monomer.UniRule annotation

Protein-protein interaction databases

STRINGi395965.Msil_3847.

Structurei

3D structure databases

ProteinModelPortaliB8EMQ0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 117117ToprimUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni165 – 1706Interaction with DNAUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1754.
HOGENOMiHOG000004020.
KOiK03168.
OMAiFRSAEYW.
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.
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.
RefSeqiYP_002364091.1. NC_011666.1.

Genome annotation databases

EnsemblBacteriaiACK52729; ACK52729; Msil_3847.
GeneIDi7092543.
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 .
RefSeqi YP_002364091.1. NC_011666.1.

3D structure databases

ProteinModelPortali B8EMQ0.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 395965.Msil_3847.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai ACK52729 ; ACK52729 ; Msil_3847 .
GeneIDi 7092543.
KEGGi msl:Msil_3847.
PATRICi 22603546. VBIMetSil55537_4120.

Phylogenomic databases

eggNOGi COG1754.
HOGENOMi HOG000004020.
KOi K03168.
OMAi FRSAEYW.
OrthoDBi EOG6S7XQ9.

Enzyme and pathway databases

BioCyci MSIL395965:GCND-3902-MONOMER.

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.
IPR013498. Topo_IA_Znf.
IPR005733. TopoI_bac-type.
IPR028612. Topoisom_1_IA.
IPR025589. Toprim_C_rpt.
IPR006171. Toprim_domain.
[Graphical view ]
PANTHERi PTHR11390. PTHR11390. 1 hit.
Pfami PF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF13368. Toprim_C_rpt. 4 hits.
PF01396. zf-C4_Topoisom. 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. 2 hits.
TIGRFAMsi TIGR01051. topA_bact. 1 hit.
PROSITEi PS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Complete genome sequence of the aerobic facultative methanotroph Methylocella silvestris BL2."
    Chen Y., Crombie A., Rahman M.T., Dedysh S.N., Liesack W., Stott M.B., Alam M., Theisen A.R., Murrell J.C., Dunfield P.F.
    J. Bacteriol. 192:3840-3841(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: BL2 / DSM 15510 / NCIMB 13906Imported.

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 26, 2014
This is version 49 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteomeImported

External Data

Dasty 3