Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

DNA topoisomerase I, plasmid

Gene

XF_a0003

Organism
Xylella fastidiosa (strain 9a5c)
Status
Reviewed-Annotation score: 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 annotation

Catalytic activityi

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

Cofactori

Mg2+UniRule annotationNote: Binds two Mg2+ per subunit.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi7 – 71Magnesium 1; catalyticUniRule annotation
Sitei31 – 311Interaction with DNAUniRule annotation
Metal bindingi79 – 791Magnesium 1; catalyticUniRule annotation
Metal bindingi79 – 791Magnesium 2UniRule annotation
Metal bindingi81 – 811Magnesium 2UniRule annotation
Sitei134 – 1341Interaction with DNAUniRule annotation
Sitei135 – 1351Interaction with DNAUniRule annotation
Sitei138 – 1381Interaction with DNAUniRule annotation
Sitei143 – 1431Interaction with DNAUniRule annotation
Active sitei287 – 2871O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation
Sitei289 – 2891Interaction with DNAUniRule annotation
Sitei483 – 4831Interaction with DNAUniRule annotation

Regions

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

GO - Molecular functioni

GO - Biological processi

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, plasmidUniRule annotation (EC:5.99.1.2UniRule annotation)
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 Componenti: Plasmid pXF51

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 660660DNA topoisomerase I, plasmidPRO_0000145174Add
BLAST

Interactioni

Subunit structurei

Monomer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliQ9PHK2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 110110ToprimUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni158 – 1636Interaction with DNAUniRule annotation

Sequence similaritiesi

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

Zinc finger

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

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_dom.
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

        10         20         30         40         50
MKLMIIESPG KIEKLSTILG DGWKIAASVG HVRDLPQKEM GVAAPDFKPS
60 70 80 90 100
YELTERGEGV VAKLKNLLKQ ADSVYLATDP DREGEAISWH LQQCLKLSNP
110 120 130 140 150
LRVTFNEITA NAVKASLVAP RTIDVKRVAA QEARRVLDRL VGYMVSPELS
160 170 180 190 200
RLTGKRLSAG RVQSPAVRLV VEREREIKAF KVTNHFGAML FFADAKTSGE
210 220 230 240 250
WSAEWLTKPK FVAEDNPYFM DRDFAAAVAQ VKAVVVKSFD ESEAKRSPPP
260 270 280 290 300
PFTTSTMQQA ASVTLGVDPK AAMDAAQKLY EQGHITYHRT DNPNVSDESL
310 320 330 340 350
GDIYAVSVKL GLDIAEKPRK FKAPAGAQVG HPAVTPTHWE VEEAGETSDQ
360 370 380 390 400
KALYKLIRLR AIACQLADAR YAVRTVRLEA AQPVGGKNVE FEARGRTLIY
410 420 430 440 450
QGWLKLIAGD QTEEEDGNEK ESSNPIPVCA PGECLDVARG KLLEKKTKPP
460 470 480 490 500
SHYTQATLVK KLESEGIGRP ATYAAIMDNI VSRGYVKTEK KYLFPTETGE
510 520 530 540 550
LIVDSLVGKF EFLDLGFTRE IEESLDRIAQ GESGYKAVIA KVHDQLNMEL
560 570 580 590 600
STLQVSATPK HPCQECGKPL RRIPGKNGHF WGCSGYPDCS VTFPDEGGKP
610 620 630 640 650
GQKKPVEVSN FACVKCGNPL KHLVKKGKGG YDFWGCSGFK EGCKATYEDK
660
KGKPNFEKAK
Length:660
Mass (Da):72,556
Last modified:October 1, 2000 - v1
Checksum:iAC4A5F000A503A1F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003851 Genomic DNA. Translation: AAF85572.1.
PIRiC82861.
RefSeqiWP_010895200.1. NC_002490.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE003851 Genomic DNA. Translation: AAF85572.1.
PIRiC82861.
RefSeqiWP_010895200.1. NC_002490.1.

3D structure databases

ProteinModelPortaliQ9PHK2.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

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_dom.
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]
ProtoNetiSearch...

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: July 22, 2015
This is version 112 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, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.