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Q9PHK2

- TOP1P_XYLFA

UniProt

Q9PHK2 - TOP1P_XYLFA

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Protein
DNA topoisomerase I, plasmid
Gene
XF_a0003
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 bindingi7 – 71Magnesium 1; catalytic By similarity
Sitei31 – 311Interaction with DNA By similarity
Metal bindingi79 – 791Magnesium 1; catalytic By similarity
Metal bindingi79 – 791Magnesium 2 By similarity
Metal bindingi81 – 811Magnesium 2 By similarity
Sitei134 – 1341Interaction with DNA By similarity
Sitei135 – 1351Interaction with DNA By similarity
Sitei138 – 1381Interaction with DNA By similarity
Sitei143 – 1431Interaction with DNA By similarity
Active sitei287 – 2871O-(5'-phospho-DNA)-tyrosine intermediate By similarity
Sitei289 – 2891Interaction with DNA By similarity
Sitei483 – 4831Interaction with DNA By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri563 – 58927C4-type 1UniRule annotation
Add
BLAST
Zinc fingeri613 – 64331C4-type 2UniRule annotation
Add
BLAST

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, Topoisomerase

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase I, plasmid (EC:5.99.1.2)
Alternative name(s):
Omega-protein
Relaxing enzyme
Swivelase
Untwisting enzyme
Gene namesi
Ordered Locus Names:XF_a0003
Encoded oniPlasmid pXF510 Publication
OrganismiXylella fastidiosa (strain 9a5c)
Taxonomic identifieri160492 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXylella
ProteomesiUP000000812: Plasmid pXF51

Subcellular locationi

GO - Cellular componenti

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 660660DNA topoisomerase I, plasmidUniRule annotation
PRO_0000145174Add
BLAST

Interactioni

Subunit structurei

Monomer By similarity.UniRule annotation

Protein-protein interaction databases

STRINGi160492.XFa0003.

Structurei

3D structure databases

ProteinModelPortaliQ9PHK2.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 110110Toprim
Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni158 – 1636Interaction with DNA By similarity

Sequence similaritiesi

Contains 1 Toprim domain.

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG0551.
KOiK03168.
OMAiHRTDNPN.
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.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. 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.

Q9PHK2-1 [UniParc]FASTAAdd to Basket

« Hide

MKLMIIESPG KIEKLSTILG DGWKIAASVG HVRDLPQKEM GVAAPDFKPS    50
YELTERGEGV VAKLKNLLKQ ADSVYLATDP DREGEAISWH LQQCLKLSNP 100
LRVTFNEITA NAVKASLVAP RTIDVKRVAA QEARRVLDRL VGYMVSPELS 150
RLTGKRLSAG RVQSPAVRLV VEREREIKAF KVTNHFGAML FFADAKTSGE 200
WSAEWLTKPK FVAEDNPYFM DRDFAAAVAQ VKAVVVKSFD ESEAKRSPPP 250
PFTTSTMQQA ASVTLGVDPK AAMDAAQKLY EQGHITYHRT DNPNVSDESL 300
GDIYAVSVKL GLDIAEKPRK FKAPAGAQVG HPAVTPTHWE VEEAGETSDQ 350
KALYKLIRLR AIACQLADAR YAVRTVRLEA AQPVGGKNVE FEARGRTLIY 400
QGWLKLIAGD QTEEEDGNEK ESSNPIPVCA PGECLDVARG KLLEKKTKPP 450
SHYTQATLVK KLESEGIGRP ATYAAIMDNI VSRGYVKTEK KYLFPTETGE 500
LIVDSLVGKF EFLDLGFTRE IEESLDRIAQ GESGYKAVIA KVHDQLNMEL 550
STLQVSATPK HPCQECGKPL RRIPGKNGHF WGCSGYPDCS VTFPDEGGKP 600
GQKKPVEVSN FACVKCGNPL KHLVKKGKGG YDFWGCSGFK EGCKATYEDK 650
KGKPNFEKAK 660
Length:660
Mass (Da):72,556
Last modified:October 1, 2000 - v1
Checksum:iAC4A5F000A503A1F
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE003851 Genomic DNA. Translation: AAF85572.1.
PIRiC82861.
RefSeqiNP_061659.1. NC_002490.1.

Genome annotation databases

EnsemblBacteriaiAAF85572; AAF85572; XF_a0003.
GeneIDi1125448.
KEGGixfa:XFa0003.
PATRICi24135901. VBIXylFas578_2957.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AE003851 Genomic DNA. Translation: AAF85572.1 .
PIRi C82861.
RefSeqi NP_061659.1. NC_002490.1.

3D structure databases

ProteinModelPortali Q9PHK2.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 160492.XFa0003.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAF85572 ; AAF85572 ; XF_a0003 .
GeneIDi 1125448.
KEGGi xfa:XFa0003.
PATRICi 24135901. VBIXylFas578_2957.

Phylogenomic databases

eggNOGi COG0551.
KOi K03168.
OMAi HRTDNPN.
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.
IPR013498. Topo_IA_Znf.
IPR005733. TopoI_bac-type.
IPR028612. Topoisom_1_IA.
IPR006171. Toprim_domain.
[Graphical view ]
PANTHERi PTHR11390. PTHR11390. 1 hit.
Pfami 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

« Hide 'large scale' publications
  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.
  2. "Genetic organization of Plasmid pXF51 from the plant pathogen Xylella fastidiosa."
    Marques M.V., da Silva A.M., Gomes S.L.
    Plasmid 45:184-199(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISCUSSION OF SEQUENCE.

Entry informationi

Entry nameiTOP1P_XYLFA
AccessioniPrimary (citable) accession number: Q9PHK2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 20, 2001
Last sequence update: October 1, 2000
Last modified: September 3, 2014
This is version 103 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, Plasmid

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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