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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)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

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
Proteomesi
  • UP000000812 Componenti: Plasmid pXF51

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

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

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.
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
Contains 1 Toprim domain.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.
Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00952. Topoisom_1_prok. 1 hit.
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. 2 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.

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.
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:XF_a0003.
PATRICi24135901. VBIXylFas578_2957.

Phylogenomic databases

KOiK03168.
OMAiHRTDNPN.
OrthoDBiPOG091H02BN.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00952. Topoisom_1_prok. 1 hit.
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. 2 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]
ProtoNetiSearch...

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: October 5, 2016
This is version 116 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

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 one 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.