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B8EMQ0

- B8EMQ0_METSB

UniProt

B8EMQ0 - B8EMQ0_METSB

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Protein
DNA topoisomerase 1
Gene
topA, Msil_3847
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 By similarity.UniRule annotationSAAS annotations

Catalytic activityi

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

Cofactori

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

Sites

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

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, TopoisomeraseUniRule annotationSAAS annotations

Keywords - Ligandi

ATP-bindingUniRule annotation, DNA-bindingUniRule annotationSAAS annotations, MagnesiumUniRule annotationSAAS annotations, Metal-bindingUniRule annotationSAAS annotations, Nucleotide-binding

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 I
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 By similarity.UniRule annotation

Protein-protein interaction databases

STRINGi395965.Msil_3847.

Structurei

3D structure databases

ProteinModelPortaliB8EMQ0.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 117117Toprim By similarityUniRule annotation
Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni165 – 1706Interaction with DNA By similarityUniRule annotation

Sequence similaritiesi

Contains 1 Toprim domain.UniRule annotation
Contains Toprim domain.SAAS annotations

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.
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

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MYVVIVESPA KAKSINKYLG KGYEVYPSYG HVRDLPAKDG SVDPDADFAM    50
LWDVDVKSAK RLNEIARAVK DADKIILATD PDREGEAISW HVLEVLKAKK 100
VLKDKPVERV VFNAITKSAV LEAMQHPRQI DVALVDAYLA RRALDYLVGF 150
NLSPVLWRKL PGARSAGRVQ SVALRLVCDR ELEIEAFVAR EYWSIVAHLR 200
TQADAPFTAR LVGADGKKIT RLDVGTGAEA AAFKTDLENA TFRVAEIEAK 250
PAKRHPSAPF TTSTLQQEAS RKLGFAPART MQLAQRLYEG ADIDGETVGL 300
ITYMRTDGVD LAPEAITSAR SVIARQFGDA YVPKAPRKYT VKAKNAQEAH 350
EAIRPTDLAR LPRAVARALE PDQAKLYELI WTRTIASQME SAELERTTVD 400
IEALAGARKL DLRATGQVVR FDGFLKLYQE GRDDEDDDES ARLPDMAKDE 450
RLKRERIEAD QHFTEPPPRF TEATLVKRME ELGIGRPSTY ASTLAVLRER 500
DYVRIEKKRL HPEDKGRLVT AFLEAFFARY VGYDFTADLE EKLDRVSNHE 550
IDWKQVLRDF WLDFSGALAG TKDLRTTEVL DRLNEILGPH IFPPKEDGSD 600
PRGCPSCGEG KLSLKLGKFG AFIGCSNYPE CKFTRTLAAP DGAEANGGER 650
PGVKSLGVDP DSGEEITLRD GRFGVYVQQG EGEKPKRSSL PPTIAPADLT 700
LEQAIALLSL PREVARHPES KEPIVAGIGR YGPYVQHGKT YANVAKDEDI 750
ISIGANRAID LIVAKESGLT GRRFGASESA PARVLGEHPA GGAVSVKAGR 800
YGPYVTHGKI NATLPKEADP TTLTLEGAVA LLAAKASGGG APMQGRLLGD 850
HPSGGPITVR AGRFGAYVNH GKTNATLKRD ASAETITLEE AIRLIEDKEA 900
AGGGPRKAAA PKKAAKSSAA AKKAAPNAKN KTAPANDEDP PFEPSPNRKP 950
AAKAAAAAHK KPAAKAAAAK LKQAKQA 977
Length:977
Mass (Da):106,066
Last modified:March 3, 2009 - v1
Checksum:iD99B73E5B0748473
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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.
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 13906.

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: September 3, 2014
This is version 46 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome

External Data

Dasty 3

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