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Q9PEV8

- TOP1_XYLFA

UniProt

Q9PEV8 - TOP1_XYLFA

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Protein
DNA topoisomerase 1
Gene
topA, XF_0920
Organism
Xylella fastidiosa (strain 9a5c)
Status
Reviewed - Annotation score: 4 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 annotation

Catalytic activityi

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

Cofactori

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi9 – 91Magnesium 1; catalytic By similarity
Sitei33 – 331Interaction with DNA By similarity
Metal bindingi82 – 821Magnesium 1; catalytic By similarity
Metal bindingi82 – 821Magnesium 2 By similarity
Metal bindingi84 – 841Magnesium 2 By similarity
Sitei143 – 1431Interaction with DNA By similarity
Sitei144 – 1441Interaction with DNA By similarity
Sitei147 – 1471Interaction with DNA By similarity
Sitei159 – 1591Interaction with DNA By similarity
Active sitei308 – 3081O-(5'-phospho-DNA)-tyrosine intermediate By similarity
Sitei310 – 3101Interaction with DNA By similarity
Sitei505 – 5051Interaction with DNA By similarity

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
Complete GO annotation...

GO - Biological processi

  1. DNA topological change Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 1 (EC:5.99.1.2)
Alternative name(s):
DNA topoisomerase I
Omega-protein
Relaxing enzyme
Swivelase
Untwisting enzyme
Gene namesi
Name:topA
Ordered Locus Names:XF_0920
OrganismiXylella fastidiosa (strain 9a5c)
Taxonomic identifieri160492 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXylella
ProteomesiUP000000812: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 815815DNA topoisomerase 1UniRule annotation
PRO_0000145172Add
BLAST

Interactioni

Subunit structurei

Monomer By similarity.UniRule annotation

Protein-protein interaction databases

STRINGi160492.XF0920.

Structurei

3D structure databases

ProteinModelPortaliQ9PEV8.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 119117Toprim
Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni167 – 1726Interaction with DNA By similarity

Sequence similaritiesi

Contains 1 Toprim domain.

Phylogenomic databases

eggNOGiCOG1754.
KOiK03168.
OMAiANEGYER.
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.
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. 3 hits.
[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.

Q9PEV8-1 [UniParc]FASTAAdd to Basket

« Hide

MPKHLLIVES PAKAKTINKY LGKDFTVLAS YGHVRDLVPK EGAVDPENGF    50
AMRYDLIDKN EKHVEAITKA AKTADSIYLA TDPDREGEAI SWHISEILKE 100
RGLLKDKPMQ RIVFTEITPR AIKEAIQKPR MIASDLVDAQ QARRALDYLV 150
GFNLSPVLWR KVQRGLSAGR VQSPALRMIV EREEEIEAFI TREYWSIHAE 200
CAHPAQHFSA KLIKLDGQKF EQFTITDSDT AAAAQRRIQQ VAQGRLHITD 250
VTNKERKRRP APPFITSTLQ QEASRKLGFT TRKTMQIAQK LYEGIALGEE 300
GSVGLITYMR TDSVNLSLDA LSEIRDIIAR DYGTNALPDK PNVYTTKSKN 350
AQEAHEAVRP TSALRTPTQV APYLSNEEHR LYELVWKRAV ASQMIPAILN 400
TTSVDLAAGN EHVFRATGTT VVVQGFLAVY EEGKDNKNAE DDDEGRKLPV 450
MKTGENVPLE RILTEQHFTQ PPPRYTEAAL VKALEEYGIG RPSTYASIIQ 500
TLLFRKYVDM EGRSFRPTDI GRAVSKFLAS HFTRYVDYDF TAHLEDELDA 550
ISRGEEEWIP LMKKFWVPFK ELVEDKKDSL DKTDAGSVRL LGIDPTSGKE 600
VSGRIGRFGP MVQIGTVDDE EKPRFASLRP NQSIYSISLE EAIELFKMPR 650
VLGEDQSQQV SVGIGRFGPF AKRGSTYVSL KSEDDPYTID LARATFLINE 700
KEEIARNRII KNFENSQIQV LNGRFGPYIS DGKLNGKIPK DREPASLTLE 750
EAQQLLIDTG KPARKNFSTK KTATKNETRK QTTKKRTTDA KATKKVSDKP 800
VKKQIKKRIA PNITE 815
Length:815
Mass (Da):91,803
Last modified:October 1, 2000 - v1
Checksum:i65BC01306E1EB1C5
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE003849 Genomic DNA. Translation: AAF83730.1.
PIRiB82746.
RefSeqiNP_298210.1. NC_002488.3.

Genome annotation databases

EnsemblBacteriaiAAF83730; AAF83730; XF_0920.
GeneIDi1126456.
KEGGixfa:XF0920.
PATRICi24131894. VBIXylFas578_0986.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE003849 Genomic DNA. Translation: AAF83730.1 .
PIRi B82746.
RefSeqi NP_298210.1. NC_002488.3.

3D structure databases

ProteinModelPortali Q9PEV8.
ModBasei Search...

Protein-protein interaction databases

STRINGi 160492.XF0920.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAF83730 ; AAF83730 ; XF_0920 .
GeneIDi 1126456.
KEGGi xfa:XF0920.
PATRICi 24131894. VBIXylFas578_0986.

Phylogenomic databases

eggNOGi COG1754.
KOi K03168.
OMAi ANEGYER.
OrthoDBi EOG6S7XQ9.

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.
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. 3 hits.
[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. "The genome sequence of the plant pathogen Xylella fastidiosa."
    Simpson A.J.G., Reinach F.C., Arruda P., Abreu F.A., Acencio M., Alvarenga R., Alves L.M.C., Araya J.E., Baia G.S., Baptista C.S., Barros M.H., Bonaccorsi E.D., Bordin S., Bove J.M., Briones M.R.S., Bueno M.R.P., Camargo A.A., Camargo L.E.A.
    , Carraro D.M., Carrer H., Colauto N.B., Colombo C., Costa F.F., Costa M.C.R., Costa-Neto C.M., Coutinho L.L., Cristofani M., Dias-Neto E., Docena C., El-Dorry H., Facincani A.P., Ferreira A.J.S., Ferreira V.C.A., Ferro J.A., Fraga J.S., Franca S.C., Franco M.C., Frohme M., Furlan L.R., Garnier M., Goldman G.H., Goldman M.H.S., Gomes S.L., Gruber A., Ho P.L., Hoheisel J.D., Junqueira M.L., Kemper E.L., Kitajima J.P., Krieger J.E., Kuramae E.E., Laigret F., Lambais M.R., Leite L.C.C., Lemos E.G.M., Lemos M.V.F., Lopes S.A., Lopes C.R., Machado J.A., Machado M.A., Madeira A.M.B.N., Madeira H.M.F., Marino C.L., Marques M.V., Martins E.A.L., Martins E.M.F., Matsukuma A.Y., Menck C.F.M., Miracca E.C., Miyaki C.Y., Monteiro-Vitorello C.B., Moon D.H., Nagai M.A., Nascimento A.L.T.O., Netto L.E.S., Nhani A. Jr., Nobrega F.G., Nunes L.R., Oliveira M.A., de Oliveira M.C., de Oliveira R.C., Palmieri D.A., Paris A., Peixoto B.R., Pereira G.A.G., Pereira H.A. Jr., Pesquero J.B., Quaggio R.B., Roberto P.G., Rodrigues V., de Rosa A.J.M., de Rosa V.E. Jr., de Sa R.G., Santelli R.V., Sawasaki H.E., da Silva A.C.R., da Silva A.M., da Silva F.R., Silva W.A. Jr., da Silveira J.F., Silvestri M.L.Z., Siqueira W.J., de Souza A.A., de Souza A.P., Terenzi M.F., Truffi D., Tsai S.M., Tsuhako M.H., Vallada H., Van Sluys M.A., Verjovski-Almeida S., Vettore A.L., Zago M.A., Zatz M., Meidanis J., Setubal J.C.
    Nature 406:151-159(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 9a5c.

Entry informationi

Entry nameiTOP1_XYLFA
AccessioniPrimary (citable) accession number: Q9PEV8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 16, 2003
Last sequence update: October 1, 2000
Last modified: September 3, 2014
This is version 86 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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