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D3V265

- D3V265_XENBS

UniProt

D3V265 - D3V265_XENBS

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Protein

DNA topoisomerase 1

Gene
topA, XBJ1_2289
Organism
Xenorhabdus bovienii (strain SS-2004)
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 bindingi9 – 91Magnesium 1; catalytic By similarityUniRule annotation
Sitei33 – 331Interaction with DNA By similarityUniRule annotation
Metal bindingi109 – 1091Magnesium 1; catalytic By similarityUniRule annotation
Metal bindingi109 – 1091Magnesium 2 By similarityUniRule annotation
Metal bindingi111 – 1111Magnesium 2 By similarityUniRule annotation
Sitei166 – 1661Interaction with DNA By similarityUniRule annotation
Sitei167 – 1671Interaction with DNA By similarityUniRule annotation
Sitei170 – 1701Interaction with DNA By similarityUniRule annotation
Sitei175 – 1751Interaction with DNA By similarityUniRule annotation
Sitei182 – 1821Interaction with DNA By similarityUniRule annotation
Active sitei317 – 3171O-(5'-phospho-DNA)-tyrosine intermediate By similarityUniRule annotation
Sitei319 – 3191Interaction with DNA By similarityUniRule annotation
Sitei505 – 5051Interaction 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. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: InterPro
  5. 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

BioCyciXBOV406818:GHLH-2275-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 annotationImported
Ordered Locus Names:XBJ1_2289Imported
OrganismiXenorhabdus bovienii (strain SS-2004)Imported
Taxonomic identifieri406818 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeXenorhabdus
ProteomesiUP000002045: Chromosome

Subcellular locationi

GO - Cellular componenti

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

Interactioni

Subunit structurei

Monomer By similarity.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliD3V265.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 140138Toprim By similarityUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni190 – 1956Interaction with DNA By similarityUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

HOGENOMiHOG000004018.
KOiK03168.

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.
IPR013263. TopoI_Znr_bac.
IPR028612. Topoisom_1_IA.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF08272. Topo_Zn_Ribbon. 2 hits.
PF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
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. 1 hit.
TIGRFAMsiTIGR01051. topA_bact. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

D3V265-1 [UniParc]FASTAAdd to Basket

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MGKALVIVES PAKAKTINKY LGNDYVVKSS VGHIRDLPTS GAASQKSSNS    50
STDKNKKKKD EKTALVNRMG VDPYHGWEAD YQILPGKEKV VAELKMLAEK 100
ADHIYLATDL DREGEAIAWH LREVIGGGEA RFSRVVFNEI TKNAITQAFD 150
NPGELNIDRV NAQQARRFMD RVVGYMVSPL LWKKVARGLS AGRVQSVAVR 200
LIVEREREIK AFVPEEYWQL HADLMAKGDI DLHMEVTHEG GKPFKPINAQ 250
QTQAAVSLLE KARYKVLDRE DRPTSSKPGA PFITSTLQQA ASTRLGFGVK 300
KTMMMAQRLY EAGHITYMRT DSTNLSQDAL DMVRGYINDQ FGDKYLPKTA 350
NIYSNKENSQ EAHEAIRPSS VDVMAEELKD MEADAQKLYQ LIWRQFIACQ 400
MMPAKYDSTT LTIQAGNFEL RAKGRTLRFD GWTKVMPALR KGDEDHTLPV 450
VEVGTELDLK QLSPSQHFTK PSARFSEASL VRELEKRGIG RPSTYASIIS 500
TIQDRGYVRG ENRRFYAEKM GEIVNDRLEE NFNELMSYDF TARMEDQLDH 550
VANNEANWKG VLDEFFTNFS EQLDVASKDP DEGGMRPNPM VSTSIDCPTC 600
SRPMGIRTAT TGVFLGCSGY TLSPKERCKQ TINLIPENEI LNILEGDEAE 650
TNALRARHRC KECGTAMDSY LIDNQRKLHV CGNNPACDGY EVEEGEFRIK 700
GYDGPIVECD KCGSEMHLKM GRFGKYMGCT SEECKNTRKI LRSGEVAPPK 750
EDPVPLPELP CEKSDAYFVL RDGAAGVFLA ASTFPKSRET RAPLVEELVK 800
FKDRLPEKLC YLAKAPVADP EGHKTVVRFS RKTKQQYVSS EKNGKATGWA 850
AFFVDGAWVV KEK 863
Length:863
Mass (Da):96,862
Last modified:April 20, 2010 - v1
Checksum:iBEBAEDE670B084B5
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
FN667741 Genomic DNA. Translation: CBJ81415.1.
RefSeqiYP_003468188.1. NC_013892.1.

Genome annotation databases

EnsemblBacteriaiCBJ81415; CBJ81415; XBJ1_2289.
GeneIDi8831902.
KEGGixbo:XBJ1_2289.
PATRICi35299411. VBIXenBov95754_2063.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
FN667741 Genomic DNA. Translation: CBJ81415.1 .
RefSeqi YP_003468188.1. NC_013892.1.

3D structure databases

ProteinModelPortali D3V265.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai CBJ81415 ; CBJ81415 ; XBJ1_2289 .
GeneIDi 8831902.
KEGGi xbo:XBJ1_2289.
PATRICi 35299411. VBIXenBov95754_2063.

Phylogenomic databases

HOGENOMi HOG000004018.
KOi K03168.

Enzyme and pathway databases

BioCyci XBOV406818:GHLH-2275-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.
IPR013263. TopoI_Znr_bac.
IPR028612. Topoisom_1_IA.
IPR006171. Toprim_domain.
[Graphical view ]
PANTHERi PTHR11390. PTHR11390. 1 hit.
Pfami PF08272. Topo_Zn_Ribbon. 2 hits.
PF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
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. 1 hit.
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 Xenorhabdus nematophila (strain ATCC 19061 / DSM 3370 / LMG 1036 / NCIB 9965 / AN6)."
    Goodrich-Blair H., Barbazuk B., Bode H.B., Darby C., Du Z., Forst S., Gaudriault S., Goldman B.S., Goodner B., Henkhaus J., Latreille P., Medigue C., Miller N., Norton S., Ogier J.C., Rouy Z., Slater S., Suen G.
    Submitted (FEB-2010) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: SS-2004.
  2. "The entomopathogenic bacterial endosymbionts xenorhabdus and photorhabdus: convergent lifestyles from divergent genomes."
    Chaston J.M., Suen G., Tucker S.L., Andersen A.W., Bhasin A., Bode E., Bode H.B., Brachmann A.O., Cowles C.E., Cowles K.N., Darby C., de Leon L., Drace K., Du Z., Givaudan A., Herbert Tran E.E., Jewell K.A., Knack J.J.
    , Krasomil-Osterfeld K.C., Kukor R., Lanois A., Latreille P., Leimgruber N.K., Lipke C.M., Liu R., Lu X., Martens E.C., Marri P.R., Medigue C., Menard M.L., Miller N.M., Morales-Soto N., Norton S., Ogier J.C., Orchard S.S., Park D., Park Y., Qurollo B.A., Sugar D.R., Richards G.R., Rouy Z., Slominski B., Slominski K., Snyder H., Tjaden B.C., van der Hoeven R., Welch R.D., Wheeler C., Xiang B., Barbazuk B., Gaudriault S., Goodner B., Slater S.C., Forst S., Goldman B.S., Goodrich-Blair H.
    PLoS ONE 6:e27909-e27909(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: SS-2004Imported.

Entry informationi

Entry nameiD3V265_XENBS
AccessioniPrimary (citable) accession number: D3V265
Entry historyi
Integrated into UniProtKB/TrEMBL: April 20, 2010
Last sequence update: April 20, 2010
Last modified: September 3, 2014
This is version 33 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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