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Q9PHK2 (TOP1P_XYLFA) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 100. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA topoisomerase I, plasmid

EC=5.99.1.2
Alternative name(s):
Omega-protein
Relaxing enzyme
Swivelase
Untwisting enzyme
Gene names
Ordered Locus Names:XF_a0003
Encoded onPlasmid pXF51
OrganismXylella fastidiosa (strain 9a5c) [Complete proteome] [HAMAP]
Taxonomic identifier160492 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXylella

Protein attributes

Sequence length660 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

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. HAMAP-Rule MF_00952

Catalytic activity

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining. HAMAP-Rule MF_00952

Cofactor

Magnesium. Binds two Mg2+ per subunit By similarity. HAMAP-Rule MF_00952

Subunit structure

Monomer By similarity. HAMAP-Rule MF_00952

Sequence similarities

Belongs to the type IA topoisomerase family.

Contains 1 Toprim domain.

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 660660DNA topoisomerase I, plasmid HAMAP-Rule MF_00952
PRO_0000145174

Regions

Domain1 – 110110Toprim
Zinc finger563 – 58927C4-type 1 HAMAP-Rule MF_00952
Zinc finger613 – 64331C4-type 2 HAMAP-Rule MF_00952
Region158 – 1636Interaction with DNA By similarity

Sites

Active site2871O-(5'-phospho-DNA)-tyrosine intermediate By similarity
Metal binding71Magnesium 1; catalytic By similarity
Metal binding791Magnesium 1; catalytic By similarity
Metal binding791Magnesium 2 By similarity
Metal binding811Magnesium 2 By similarity
Site311Interaction with DNA By similarity
Site1341Interaction with DNA By similarity
Site1351Interaction with DNA By similarity
Site1381Interaction with DNA By similarity
Site1431Interaction with DNA By similarity
Site2891Interaction with DNA By similarity
Site4831Interaction with DNA By similarity

Sequences

Sequence LengthMass (Da)Tools
Q9PHK2 [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: AC4A5F000A503A1F

FASTA66072,556
        10         20         30         40         50         60 
MKLMIIESPG KIEKLSTILG DGWKIAASVG HVRDLPQKEM GVAAPDFKPS YELTERGEGV 

        70         80         90        100        110        120 
VAKLKNLLKQ ADSVYLATDP DREGEAISWH LQQCLKLSNP LRVTFNEITA NAVKASLVAP 

       130        140        150        160        170        180 
RTIDVKRVAA QEARRVLDRL VGYMVSPELS RLTGKRLSAG RVQSPAVRLV VEREREIKAF 

       190        200        210        220        230        240 
KVTNHFGAML FFADAKTSGE WSAEWLTKPK FVAEDNPYFM DRDFAAAVAQ VKAVVVKSFD 

       250        260        270        280        290        300 
ESEAKRSPPP PFTTSTMQQA ASVTLGVDPK AAMDAAQKLY EQGHITYHRT DNPNVSDESL 

       310        320        330        340        350        360 
GDIYAVSVKL GLDIAEKPRK FKAPAGAQVG HPAVTPTHWE VEEAGETSDQ KALYKLIRLR 

       370        380        390        400        410        420 
AIACQLADAR YAVRTVRLEA AQPVGGKNVE FEARGRTLIY QGWLKLIAGD QTEEEDGNEK 

       430        440        450        460        470        480 
ESSNPIPVCA PGECLDVARG KLLEKKTKPP SHYTQATLVK KLESEGIGRP ATYAAIMDNI 

       490        500        510        520        530        540 
VSRGYVKTEK KYLFPTETGE LIVDSLVGKF EFLDLGFTRE IEESLDRIAQ GESGYKAVIA 

       550        560        570        580        590        600 
KVHDQLNMEL STLQVSATPK HPCQECGKPL RRIPGKNGHF WGCSGYPDCS VTFPDEGGKP 

       610        620        630        640        650        660 
GQKKPVEVSN FACVKCGNPL KHLVKKGKGG YDFWGCSGFK EGCKATYEDK KGKPNFEKAK 

« Hide

References

« Hide 'large scale' references
[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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE003851 Genomic DNA. Translation: AAF85572.1.
PIRC82861.
RefSeqNP_061659.1. NC_002490.1.

3D structure databases

ProteinModelPortalQ9PHK2.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING160492.XFa0003.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAF85572; AAF85572; XF_a0003.
GeneID1125448.
KEGGxfa:XFa0003.
PATRIC24135901. VBIXylFas578_2957.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0551.
KOK03168.
OMAHRTDNPN.
OrthoDBEOG6S7XQ9.
ProtClustDBCLSK540625.

Family and domain databases

Gene3D1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPMF_00952. Topoisom_1_prok.
InterProIPR000380. 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]
PANTHERPTHR11390. PTHR11390. 1 hit.
PfamPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF01396. zf-C4_Topoisom. 1 hit.
[Graphical view]
PRINTSPR00417. PRTPISMRASEI.
SMARTSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMSSF56712. SSF56712. 1 hit.
TIGRFAMsTIGR01051. topA_bact. 1 hit.
PROSITEPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameTOP1P_XYLFA
AccessionPrimary (citable) accession number: Q9PHK2
Entry history
Integrated into UniProtKB/Swiss-Prot: June 20, 2001
Last sequence update: October 1, 2000
Last modified: February 19, 2014
This is version 100 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families