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Protein

DNA topoisomerase I, plasmid

Gene

XF_a0003

Organism
Xylella fastidiosa (strain 9a5c)
Status
Reviewed-Annotation score: -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)DescriptionActionsGraphical viewLength
Metal bindingi7Magnesium 1; catalyticUniRule annotation1
Metal bindingi79Magnesium 1; catalyticUniRule annotation1
Metal bindingi79Magnesium 2UniRule annotation1
Metal bindingi81Magnesium 2UniRule annotation1
Active sitei287O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri563 – 589C4-type 1Add BLAST27
Zinc fingeri613 – 643C4-type 2Add BLAST31

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Isomerase, Topoisomerase
LigandMagnesium, 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
Proteomesi
  • UP000000812 Componenti: Plasmid pXF51

Subcellular locationi

GO - Cellular componenti

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001451741 – 660DNA topoisomerase I, plasmidAdd BLAST660

Proteomic databases

PRIDEiQ9PHK2

Interactioni

Subunit structurei

Monomer.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei31Interaction with DNAUniRule annotation1
Sitei134Interaction with DNAUniRule annotation1
Sitei135Interaction with DNAUniRule annotation1
Sitei138Interaction with DNAUniRule annotation1
Sitei143Interaction with DNAUniRule annotation1
Sitei289Interaction with DNAUniRule annotation1
Sitei483Interaction with DNAUniRule annotation1

Structurei

3D structure databases

ProteinModelPortaliQ9PHK2
SMRiQ9PHK2
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 110ToprimUniRule annotationAdd BLAST110

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni158 – 163Interaction with DNAUniRule annotation6

Sequence similaritiesi

Belongs to the type IA topoisomerase family.UniRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri563 – 589C4-type 1Add BLAST27
Zinc fingeri613 – 643C4-type 2Add BLAST31

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

KOiK03168
OMAiHRTDNPN
OrthoDBiPOG091H02BN

Family and domain databases

CDDicd00186 TOP1Ac, 1 hit
cd03363 TOPRIM_TopoIA_TopoI, 1 hit
Gene3Di1.10.290.10, 1 hit
1.10.460.10, 2 hits
2.70.20.10, 2 hits
HAMAPiMF_00952 Topoisom_1_prok, 1 hit
InterProiView protein in InterPro
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
IPR013826 Topo_IA_cen_sub3
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
IPR034149 TOPRIM_TopoI
PANTHERiPTHR42785 PTHR42785, 1 hit
PfamiView protein in Pfam
PF01131 Topoisom_bac, 1 hit
PF01751 Toprim, 1 hit
PF01396 zf-C4_Topoisom, 2 hits
PRINTSiPR00417 PRTPISMRASEI
SMARTiView protein in SMART
SM00437 TOP1Ac, 1 hit
SM00436 TOP1Bc, 1 hit
SM00493 TOPRIM, 1 hit
SUPFAMiSSF56712 SSF56712, 1 hit
TIGRFAMsiTIGR01051 topA_bact, 1 hit
PROSITEiView protein in PROSITE
PS00396 TOPOISOMERASE_I_PROK, 1 hit
PS50880 TOPRIM, 1 hit

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:XF_a0003

Similar proteinsi

Entry informationi

Entry nameiTOP1P_XYLFA
AccessioniPrimary (citable) accession number: Q9PHK2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 20, 2001
Last sequence update: October 1, 2000
Last modified: May 23, 2018
This is version 123 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Plasmid, Reference proteome

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