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Protein

DNA topoisomerase 3-alpha

Gene

TOP3A

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: -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)DescriptionActionsGraphical viewLength
Metal bindingi16Magnesium 1; catalyticPROSITE-ProRule annotation1
Metal bindingi123Magnesium 1; catalyticPROSITE-ProRule annotation1
Metal bindingi123Magnesium 2PROSITE-ProRule annotation1
Metal bindingi125Magnesium 2PROSITE-ProRule annotation1
Active sitei342O-(5'-phospho-DNA)-tyrosine intermediateBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri642 – 670C4-typeSequence analysisAdd BLAST29
Zinc fingeri767 – 782CCHC-type 1PROSITE-ProRule annotationAdd BLAST16
Zinc fingeri901 – 917CCHC-type 2PROSITE-ProRule annotationAdd BLAST17

GO - Molecular functioni

GO - Biological processi

  • chromosome segregation Source: TAIR
  • DNA repair Source: TAIR
  • DNA topological change Source: GO_Central
  • meiotic cell cycle Source: TAIR
  • mitotic cell cycle Source: TAIR
  • resolution of meiotic recombination intermediates Source: TAIR

Keywordsi

Molecular functionDNA-binding, Isomerase, Topoisomerase
Biological processMeiosis
LigandMagnesium, Metal-binding, Zinc

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

AraportiAT5G63920
TAIRilocus:2160841 AT5G63920

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

Pathology & Biotechi

Disruption phenotypei

Severe developmental defects and early lethality.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004297711 – 926DNA topoisomerase 3-alphaAdd BLAST926

Proteomic databases

PaxDbiQ9LVP1
PRIDEiQ9LVP1

PTM databases

iPTMnetiQ9LVP1

Expressioni

Gene expression databases

ExpressionAtlasiQ9LVP1 baseline and differential
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)DescriptionActionsGraphical viewLength
Sitei80Interaction with DNAPROSITE-ProRule annotation1
Sitei195Interaction with DNAPROSITE-ProRule annotation1
Sitei202Interaction with DNAPROSITE-ProRule annotation1
Sitei344Interaction with DNAPROSITE-ProRule annotation1

Protein-protein interaction databases

STRINGi3702.AT5G63920.1

Structurei

3D structure databases

ProteinModelPortaliQ9LVP1
SMRiQ9LVP1
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini10 – 154ToprimPROSITE-ProRule annotationAdd BLAST145

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni219 – 224Interaction with DNABy similarity6

Sequence similaritiesi

Belongs to the type IA topoisomerase family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri642 – 670C4-typeSequence analysisAdd BLAST29
Zinc fingeri767 – 782CCHC-type 1PROSITE-ProRule annotationAdd BLAST16
Zinc fingeri901 – 917CCHC-type 2PROSITE-ProRule annotationAdd BLAST17

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1956 Eukaryota
COG0550 LUCA
HOGENOMiHOG000184377
InParanoidiQ9LVP1
KOiK03165
OMAiFKAIQAF
OrthoDBiEOG093601SW
PhylomeDBiQ9LVP1

Family and domain databases

CDDicd00186 TOP1Ac, 1 hit
cd03362 TOPRIM_TopoIA_TopoIII, 1 hit
Gene3Di1.10.290.10, 1 hit
1.10.460.10, 2 hits
2.70.20.10, 2 hits
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
IPR006171 TOPRIM_domain
IPR034144 TOPRIM_TopoIII
IPR001878 Znf_CCHC
IPR036875 Znf_CCHC_sf
IPR010666 Znf_GRF
PANTHERiPTHR11390 PTHR11390, 1 hit
PfamiView protein in Pfam
PF01131 Topoisom_bac, 1 hit
PF01751 Toprim, 1 hit
PF01396 zf-C4_Topoisom, 1 hit
PF06839 zf-GRF, 1 hit
PRINTSiPR00417 PRTPISMRASEI
SMARTiView protein in SMART
SM00437 TOP1Ac, 1 hit
SM00436 TOP1Bc, 1 hit
SM00493 TOPRIM, 1 hit
SM00343 ZnF_C2HC, 2 hits
SUPFAMiSSF56712 SSF56712, 1 hit
SSF57756 SSF57756, 2 hits
PROSITEiView protein in PROSITE
PS00396 TOPOISOMERASE_I_PROK, 1 hit
PS50880 TOPRIM, 1 hit
PS50158 ZF_CCHC, 2 hits

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_125788.7
UniGeneiAt.28974

Genome annotation databases

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

Similar proteinsi

Entry informationi

Entry nameiTOP3A_ARATH
AccessioniPrimary (citable) accession number: Q9LVP1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 9, 2014
Last sequence update: October 1, 2000
Last modified: April 25, 2018
This is version 115 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
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Main funding by: National Institutes of Health