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Protein

DNA topoisomerase 1

Gene

topA

Organism
Xylella fastidiosa (strain Temecula1 / ATCC 700964)
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 bindingi9Magnesium 1; catalyticUniRule annotation1
Metal bindingi82Magnesium 1; catalyticUniRule annotation1
Metal bindingi82Magnesium 2UniRule annotation1
Metal bindingi84Magnesium 2UniRule annotation1
Active sitei308O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 1UniRule annotation (EC:5.99.1.2UniRule annotation)
Alternative name(s):
DNA topoisomerase IUniRule annotation
Omega-protein
Relaxing enzyme
Swivelase
Untwisting enzyme
Gene namesi
Name:topAUniRule annotation
Ordered Locus Names:PD_1767
OrganismiXylella fastidiosa (strain Temecula1 / ATCC 700964)
Taxonomic identifieri183190 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXylella
Proteomesi
  • UP000002516 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001451731 – 815DNA topoisomerase 1Add BLAST815

Interactioni

Subunit structurei

Monomer.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei33Interaction with DNAUniRule annotation1
Sitei143Interaction with DNAUniRule annotation1
Sitei144Interaction with DNAUniRule annotation1
Sitei147Interaction with DNAUniRule annotation1
Sitei159Interaction with DNAUniRule annotation1
Sitei310Interaction with DNAUniRule annotation1
Sitei505Interaction with DNAUniRule annotation1

Structurei

3D structure databases

ProteinModelPortaliQ87AQ6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini3 – 119ToprimUniRule annotationAdd BLAST117

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni167 – 172Interaction with DNAUniRule annotation6

Sequence similaritiesi

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

Phylogenomic databases

KOiK03168.
OMAiFGPFIKW.

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.
IPR005733. TopoI_bac-type.
IPR028612. Topoisom_1_IA.
IPR025589. Toprim_C_rpt.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF13368. Toprim_C_rpt. 3 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.

Q87AQ6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPKHLLIVES PAKAKTINKY LGKDFTVLAS YGHVRDLVPK EGAVDPENGF
60 70 80 90 100
AMRYDLIDKN EKHVEAITKA AKTADSIYLA TDPDREGEAI SWHISEILKE
110 120 130 140 150
RGLLKDKPMQ RIVFTEITPR AIKEAIQKPR MIASDLVDAQ QARRALDYLV
160 170 180 190 200
GFNLSPVLWR KVQRGLSAGR VQSPALRMIV EREEEIEAFI TREYWSIHAE
210 220 230 240 250
CTHPAQHFSA KLIKLDGKKF EQFTITDSDT AAAAQRRIQQ AAQGRLHITD
260 270 280 290 300
VTNKERKRRP APPFITSTLQ QEASRKLGFT TRKTMQIAQK LYEGIALGEE
310 320 330 340 350
GSVGLITYMR TDSVNLSLDA LSEIRDIIAR DYGTNALPDK PNVYTTKSKN
360 370 380 390 400
AQEAHEAVRP TSALRTPTQV APYLSNEEHR LYELVWKRTV ASQMIPAILN
410 420 430 440 450
TTSVDLAAGN EHVFRATGTT VVVQGFLAVY EEGKDNKNAE DDDEGRKLPV
460 470 480 490 500
MKTGENVPLE RILTEQHFTQ PPPRYTEAAL VKALEEYGIG RPSTYASIIQ
510 520 530 540 550
TLLFRKYVDM EGRSFRPTDI GRAVSKFLSS HFTQYVDYDF TAHLEDELDA
560 570 580 590 600
ISRGEEEWIP LMKKFWVPFK ELVEDKKDSL DKTDAGSVRL LGIDPTSGKE
610 620 630 640 650
VSARIGRFGP MVQIGTVDDE EKPRFASLRP NQSIYSISLE EAIELFKMPR
660 670 680 690 700
VLGEDQSQQV SVGIGRFGPF AKRGSTYVSL KSEDDPYTID LARATLLINE
710 720 730 740 750
KEEIARNRII KDFENSQIQV LNGRFGPYIS DGKLNGKIPK DREPASLTLE
760 770 780 790 800
EAQQLLINTG KPARKNFSTK KTATKNETRK QTTKKRTTDA KATKKVSDKP
810
VKKQIKKRIA PNITQ
Length:815
Mass (Da):91,802
Last modified:June 16, 2003 - v1
Checksum:i2F23C4675BEA8363
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009442 Genomic DNA. Translation: AAO29601.1.
RefSeqiWP_004089635.1. NC_004556.1.

Genome annotation databases

EnsemblBacteriaiAAO29601; AAO29601; PD_1767.
KEGGixft:PD_1767.
PATRICi24151979. VBIXylFas71109_2289.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE009442 Genomic DNA. Translation: AAO29601.1.
RefSeqiWP_004089635.1. NC_004556.1.

3D structure databases

ProteinModelPortaliQ87AQ6.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAO29601; AAO29601; PD_1767.
KEGGixft:PD_1767.
PATRICi24151979. VBIXylFas71109_2289.

Phylogenomic databases

KOiK03168.
OMAiFGPFIKW.

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.
IPR005733. TopoI_bac-type.
IPR028612. Topoisom_1_IA.
IPR025589. Toprim_C_rpt.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF13368. Toprim_C_rpt. 3 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 nameiTOP1_XYLFT
AccessioniPrimary (citable) accession number: Q87AQ6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 16, 2003
Last sequence update: June 16, 2003
Last modified: November 2, 2016
This is version 95 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

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.