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D3V265

- D3V265_XENBS

UniProt

D3V265 - D3V265_XENBS

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Protein

DNA topoisomerase 1

Gene

topA

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.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 bindingi9 – 91Magnesium 1; catalyticUniRule annotation
Sitei33 – 331Interaction with DNAUniRule annotation
Metal bindingi109 – 1091Magnesium 1; catalyticUniRule annotation
Metal bindingi109 – 1091Magnesium 2UniRule annotation
Metal bindingi111 – 1111Magnesium 2UniRule annotation
Sitei166 – 1661Interaction with DNAUniRule annotation
Sitei167 – 1671Interaction with DNAUniRule annotation
Sitei170 – 1701Interaction with DNAUniRule annotation
Sitei175 – 1751Interaction with DNAUniRule annotation
Sitei182 – 1821Interaction with DNAUniRule annotation
Active sitei317 – 3171O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation
Sitei319 – 3191Interaction with DNAUniRule annotation
Sitei505 – 5051Interaction with DNAUniRule annotation

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-KW
  2. DNA topoisomerase type I activity Source: UniProtKB-HAMAP
  3. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: InterPro
  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 annotation

Keywords - Ligandi

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

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 IUniRule annotation
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.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliD3V265.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 140138ToprimUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni190 – 1956Interaction 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

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_dom.
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

« Hide

        10         20         30         40         50
MGKALVIVES PAKAKTINKY LGNDYVVKSS VGHIRDLPTS GAASQKSSNS
60 70 80 90 100
STDKNKKKKD EKTALVNRMG VDPYHGWEAD YQILPGKEKV VAELKMLAEK
110 120 130 140 150
ADHIYLATDL DREGEAIAWH LREVIGGGEA RFSRVVFNEI TKNAITQAFD
160 170 180 190 200
NPGELNIDRV NAQQARRFMD RVVGYMVSPL LWKKVARGLS AGRVQSVAVR
210 220 230 240 250
LIVEREREIK AFVPEEYWQL HADLMAKGDI DLHMEVTHEG GKPFKPINAQ
260 270 280 290 300
QTQAAVSLLE KARYKVLDRE DRPTSSKPGA PFITSTLQQA ASTRLGFGVK
310 320 330 340 350
KTMMMAQRLY EAGHITYMRT DSTNLSQDAL DMVRGYINDQ FGDKYLPKTA
360 370 380 390 400
NIYSNKENSQ EAHEAIRPSS VDVMAEELKD MEADAQKLYQ LIWRQFIACQ
410 420 430 440 450
MMPAKYDSTT LTIQAGNFEL RAKGRTLRFD GWTKVMPALR KGDEDHTLPV
460 470 480 490 500
VEVGTELDLK QLSPSQHFTK PSARFSEASL VRELEKRGIG RPSTYASIIS
510 520 530 540 550
TIQDRGYVRG ENRRFYAEKM GEIVNDRLEE NFNELMSYDF TARMEDQLDH
560 570 580 590 600
VANNEANWKG VLDEFFTNFS EQLDVASKDP DEGGMRPNPM VSTSIDCPTC
610 620 630 640 650
SRPMGIRTAT TGVFLGCSGY TLSPKERCKQ TINLIPENEI LNILEGDEAE
660 670 680 690 700
TNALRARHRC KECGTAMDSY LIDNQRKLHV CGNNPACDGY EVEEGEFRIK
710 720 730 740 750
GYDGPIVECD KCGSEMHLKM GRFGKYMGCT SEECKNTRKI LRSGEVAPPK
760 770 780 790 800
EDPVPLPELP CEKSDAYFVL RDGAAGVFLA ASTFPKSRET RAPLVEELVK
810 820 830 840 850
FKDRLPEKLC YLAKAPVADP EGHKTVVRFS RKTKQQYVSS EKNGKATGWA
860
AFFVDGAWVV KEK
Length:863
Mass (Da):96,862
Last modified:April 20, 2010 - v1
Checksum:iBEBAEDE670B084B5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
FN667741 Genomic DNA. Translation: CBJ81415.1.
RefSeqiWP_012988731.1. NC_013892.1.
YP_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:
EMBLi
GenBanki
DDBJi
Links Updated
FN667741 Genomic DNA. Translation: CBJ81415.1 .
RefSeqi WP_012988731.1. NC_013892.1.
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_dom.
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-2004Imported.
  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: November 26, 2014
This is version 36 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