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Protein

DNA topoisomerase 3-alpha

Gene

TOP3A

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Releases the supercoiling and torsional tension of DNA 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. Essential component of the RMI complex, a complex that plays an important role in the resolution step of homologous recombination, in a process called Holliday Junction dissolution, to limit DNA crossover formation in cells. Together with RMI1, is essential for the resolution of meiotic recombination intermediates, a step that prevents entanglement of the parental chromosomes. May have DNA decatenation activity.1 Publication

Catalytic activityi

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

Cofactori

Mg2+By similarityNote: Binds two Mg2+ ions per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi16 – 161Magnesium 1; catalyticPROSITE-ProRule annotation
Metal bindingi123 – 1231Magnesium 1; catalyticPROSITE-ProRule annotation
Metal bindingi123 – 1231Magnesium 2PROSITE-ProRule annotation
Metal bindingi125 – 1251Magnesium 2PROSITE-ProRule annotation
Active sitei342 – 3421O-(5'-phospho-DNA)-tyrosine intermediateBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri642 – 67029C4-typeSequence analysisAdd
BLAST
Zinc fingeri767 – 78216CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri901 – 91717CCHC-type 2PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • chromosome segregation Source: TAIR
  • DNA repair Source: TAIR
  • DNA topological change Source: InterPro
  • meiotic nuclear division Source: TAIR
  • mitotic nuclear division Source: TAIR
  • resolution of meiotic recombination intermediates Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Biological processi

Meiosis

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciARA:AT5G63920-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 3-alpha (EC:5.99.1.2)
Gene namesi
Name:TOP3A
Ordered Locus Names:At5g63920
ORF Names:MGI19.16
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G63920.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Disruption phenotypei

Severe developmental defects and early lethality.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 926926DNA topoisomerase 3-alphaPRO_0000429771Add
BLAST

Proteomic databases

PaxDbiQ9LVP1.
PRIDEiQ9LVP1.

PTM databases

iPTMnetiQ9LVP1.

Expressioni

Gene expression databases

GenevisibleiQ9LVP1. AT.

Interactioni

Subunit structurei

Component of the RMI complex, containing at least TOP3A and RMI1. The RMI complex interacts with RECQL4A (By similarity).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei80 – 801Interaction with DNAPROSITE-ProRule annotation
Sitei195 – 1951Interaction with DNAPROSITE-ProRule annotation
Sitei202 – 2021Interaction with DNAPROSITE-ProRule annotation
Sitei344 – 3441Interaction with DNAPROSITE-ProRule annotation

Protein-protein interaction databases

STRINGi3702.AT5G63920.1.

Structurei

3D structure databases

ProteinModelPortaliQ9LVP1.
SMRiQ9LVP1. Positions 7-621.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini10 – 154145ToprimPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni219 – 2246Interaction with DNABy similarity

Sequence similaritiesi

Belongs to the type IA topoisomerase family.Curated
Contains 2 CCHC-type zinc fingers.PROSITE-ProRule annotation
Contains 1 Toprim domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri642 – 67029C4-typeSequence analysisAdd
BLAST
Zinc fingeri767 – 78216CCHC-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri901 – 91717CCHC-type 2PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1956. Eukaryota.
COG0550. LUCA.
HOGENOMiHOG000184377.
InParanoidiQ9LVP1.
KOiK03165.
OMAiGSVPPTM.
OrthoDBiEOG093601SW.
PhylomeDBiQ9LVP1.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.290.10. 1 hit.
1.10.460.10. 2 hits.
3.40.50.140. 1 hit.
InterProiIPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR023406. Topo_IA_AS.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013826. Topo_IA_cen_sub3.
IPR023405. Topo_IA_core_domain.
IPR003602. Topo_IA_DNA-bd_dom.
IPR013498. Topo_IA_Znf.
IPR006171. Toprim_domain.
IPR001878. Znf_CCHC.
IPR010666. Znf_GRF.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 2 hits.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF01396. zf-C4_Topoisom. 1 hit.
PF06839. zf-GRF. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
SM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 1 hit.
SSF57756. SSF57756. 2 hits.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
PS50158. ZF_CCHC. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9LVP1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSRRGGGPVT VLNVAEKPSV AKSVAGILSR GTFRTREGRS RYNKIFEFDY
60 70 80 90 100
AINGQPCRML MTSVIGHLME LEFADRYRKW HSCDPADLYQ APVMKHVPED
110 120 130 140 150
KKDIKKTLEE EARKSDWLVL WLDCDREGEN IAFEVVDVCR AVKHNLFIRR
160 170 180 190 200
AHFSALIDRD IHEAVQNLRD PNQLFAEAVD ARQEIDLRIG ASFTRFQTML
210 220 230 240 250
LRDRFAIDST GEERSRVISY GPCQFPTLGF IVERYWEIQA HEPEEFWTIN
260 270 280 290 300
CSHQSEEGLA TFNWMRGHLF DYASAVILYE MCVEEPTATV MNVPHPRERF
310 320 330 340 350
KYPPYPLNTI ELEKRASRYF RLSSEHTMKV AEELYQAGFI SYPRTETDSF
360 370 380 390 400
SSRTDLRAMV EEQTRHPAWG SYAQRLLEPE GGLWRNPANG GHDDKAHPPI
410 420 430 440 450
HPTKFSSGES NWSRDHLNVY ELVVRHYLAC VSQPAVAAET TVEIDIAGER
460 470 480 490 500
FSASGRAILA KNYLEVYRFE SWGGSVIPVY EKGQQFIPTT LTLDAAVTRP
510 520 530 540 550
PPLLCEADLL SCMDKAGIGT DATMHDHIKK LLDRGYATKD ANTRFSPTNL
560 570 580 590 600
GEALVMGYDD MGYELWKPNL RALMEHDMNE VSVGRKTKAE VLETCLQQMK
610 620 630 640 650
ACFLDARVKK SKLLEAMTIF FERSNNTDES ESQTAGEVVR RCNLCNESDM
660 670 680 690 700
ALRKNRDGNF MVGCMNYPQC RNAVWLPGPT LEASVTTNVC QSCGPGPVYK
710 720 730 740 750
ILFKFRQIGI PPGFDVNHLG CVGGCDDILK QLIDICGTGS RSQARRTPGT
760 770 780 790 800
APSNNIQGSN TRQSNVCIHC QQRGHASTNC PSRVPASRNS RPTATNPRND
810 820 830 840 850
ESTVSCNTCG SQCVLRTANT EANRGRQFFS CPTQGCSFFA WEDSINNSSG
860 870 880 890 900
NATTGSNSGG SGRRGSRGRG RGGRGGQSSG GRRGSGTSFV SATGEPVSGI
910 920
RCFSCGDPSH FANACPNRNN SNGNYF
Length:926
Mass (Da):103,407
Last modified:October 1, 2000 - v1
Checksum:i806A59EAD08CBB08
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EU295446 mRNA. Translation: ACA50279.1.
AB019227 Genomic DNA. Translation: BAA96895.1.
CP002688 Genomic DNA. Translation: AED97816.1.
RefSeqiNP_201197.1. NM_125788.6.
UniGeneiAt.28974.

Genome annotation databases

EnsemblPlantsiAT5G63920.1; AT5G63920.1; AT5G63920.
GeneIDi836513.
GrameneiAT5G63920.1; AT5G63920.1; AT5G63920.
KEGGiath:AT5G63920.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
EU295446 mRNA. Translation: ACA50279.1.
AB019227 Genomic DNA. Translation: BAA96895.1.
CP002688 Genomic DNA. Translation: AED97816.1.
RefSeqiNP_201197.1. NM_125788.6.
UniGeneiAt.28974.

3D structure databases

ProteinModelPortaliQ9LVP1.
SMRiQ9LVP1. Positions 7-621.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT5G63920.1.

PTM databases

iPTMnetiQ9LVP1.

Proteomic databases

PaxDbiQ9LVP1.
PRIDEiQ9LVP1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G63920.1; AT5G63920.1; AT5G63920.
GeneIDi836513.
GrameneiAT5G63920.1; AT5G63920.1; AT5G63920.
KEGGiath:AT5G63920.

Organism-specific databases

TAIRiAT5G63920.

Phylogenomic databases

eggNOGiKOG1956. Eukaryota.
COG0550. LUCA.
HOGENOMiHOG000184377.
InParanoidiQ9LVP1.
KOiK03165.
OMAiGSVPPTM.
OrthoDBiEOG093601SW.
PhylomeDBiQ9LVP1.

Enzyme and pathway databases

BioCyciARA:AT5G63920-MONOMER.

Miscellaneous databases

PROiQ9LVP1.

Gene expression databases

GenevisibleiQ9LVP1. AT.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.290.10. 1 hit.
1.10.460.10. 2 hits.
3.40.50.140. 1 hit.
InterProiIPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR023406. Topo_IA_AS.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013826. Topo_IA_cen_sub3.
IPR023405. Topo_IA_core_domain.
IPR003602. Topo_IA_DNA-bd_dom.
IPR013498. Topo_IA_Znf.
IPR006171. Toprim_domain.
IPR001878. Znf_CCHC.
IPR010666. Znf_GRF.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 2 hits.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF01396. zf-C4_Topoisom. 1 hit.
PF06839. zf-GRF. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
SM00343. ZnF_C2HC. 2 hits.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 1 hit.
SSF57756. SSF57756. 2 hits.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
PS50158. ZF_CCHC. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTOP3A_ARATH
AccessioniPrimary (citable) accession number: Q9LVP1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 9, 2014
Last sequence update: October 1, 2000
Last modified: September 7, 2016
This is version 101 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. 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.