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Protein

DNA topoisomerase 3-beta-1

Gene

TOP3B

Organism
Homo sapiens (Human)
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 than 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 (By similarity). Possesses negatively supercoiled DNA relaxing activity.By similarity

Catalytic activityi

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei336O-(5'-phospho-DNA)-tyrosine intermediateBy similarity1

GO - Molecular functioni

  • DNA binding Source: ProtInc
  • DNA topoisomerase activity Source: GO_Central
  • DNA topoisomerase type I activity Source: UniProtKB-EC
  • RNA binding Source: UniProtKB

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Isomerase, Topoisomerase

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 3-beta-1 (EC:5.99.1.2)
Alternative name(s):
DNA topoisomerase III beta-1
Gene namesi
Name:TOP3B
Synonyms:TOP3B1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 22

Organism-specific databases

EuPathDBiHostDB:ENSG00000100038.19
HGNCiHGNC:11993 TOP3B
MIMi603582 gene
neXtProtiNX_O95985

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Pathology & Biotechi

Organism-specific databases

DisGeNETi8940
OpenTargetsiENSG00000100038
PharmGKBiPA36674

Polymorphism and mutation databases

BioMutaiTOP3B

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001451921 – 862DNA topoisomerase 3-beta-1Add BLAST862

Proteomic databases

EPDiO95985
MaxQBiO95985
PaxDbiO95985
PeptideAtlasiO95985
PRIDEiO95985
ProteomicsDBi51161
51162 [O95985-2]
51163 [O95985-3]

PTM databases

iPTMnetiO95985
PhosphoSitePlusiO95985

Expressioni

Tissue specificityi

Isoform 1 is found in testis, heart and skeletal muscle. A 4 kb transcript which probably represents isoform 2 is found in thymus, kidney and pancreas.1 Publication

Gene expression databases

BgeeiENSG00000100038 Expressed in 120 organ(s), highest expression level in dorsal plus ventral thalamus
CleanExiHS_TOP3B
ExpressionAtlasiO95985 baseline and differential
GenevisibleiO95985 HS

Organism-specific databases

HPAiHPA069678

Interactioni

Binary interactionsi

Protein-protein interaction databases

BioGridi114452, 38 interactors
ComplexPortaliCPX-1621 TDRD3-TOP3B type IA topoisomerase complex
IntActiO95985, 31 interactors
STRINGi9606.ENSP00000349705

Structurei

Secondary structure

1862
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliO95985
SMRiO95985
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini3 – 153ToprimPROSITE-ProRule annotationAdd BLAST151

Sequence similaritiesi

Belongs to the type IA topoisomerase family.Curated

Phylogenomic databases

eggNOGiKOG1956 Eukaryota
COG0550 LUCA
GeneTreeiENSGT00530000063430
HOGENOMiHOG000184378
HOVERGENiHBG059857
InParanoidiO95985
KOiK03165
OMAiTYPRVDT
OrthoDBiEOG091G01EW
PhylomeDBiO95985
TreeFamiTF105288

Family and domain databases

CDDicd00186 TOP1Ac, 1 hit
cd03362 TOPRIM_TopoIA_TopoIII, 1 hit
Gene3Di1.10.290.10, 1 hit
1.10.460.10, 1 hit
2.70.20.10, 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
IPR006171 TOPRIM_domain
IPR034144 TOPRIM_TopoIII
PANTHERiPTHR11390 PTHR11390, 1 hit
PfamiView protein in Pfam
PF01131 Topoisom_bac, 1 hit
PF01751 Toprim, 1 hit
PRINTSiPR00417 PRTPISMRASEI
SMARTiView protein in SMART
SM00437 TOP1Ac, 1 hit
SM00436 TOP1Bc, 1 hit
SM00493 TOPRIM, 1 hit
SUPFAMiSSF56712 SSF56712, 1 hit
PROSITEiView protein in PROSITE
PS00396 TOPOISOMERASE_I_PROK, 1 hit
PS50880 TOPRIM, 1 hit

Sequences (3+)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 3 described isoforms and 11 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: O95985-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MKTVLMVAEK PSLAQSIAKI LSRGSLSSHK GLNGACSVHE YTGTFAGQPV
60 70 80 90 100
RFKMTSVCGH VMTLDFLGKY NKWDKVDPAE LFSQAPTEKK EANPKLNMVK
110 120 130 140 150
FLQVEGRGCD YIVLWLDCDK EGENICFEVL DAVLPVMNKA HGGEKTVFRA
160 170 180 190 200
RFSSITDTDI CNAMACLGEP DHNEALSVDA RQELDLRIGC AFTRFQTKYF
210 220 230 240 250
QGKYGDLDSS LISFGPCQTP TLGFCVERHD KIQSFKPETY WVLQAKVNTD
260 270 280 290 300
KDRSLLLDWD RVRVFDREIA QMFLNMTKLE KEAQVEATSR KEKAKQRPLA
310 320 330 340 350
LNTVEMLRVA SSSLGMGPQH AMQTAERLYT QGYISYPRTE TTHYPENFDL
360 370 380 390 400
KGSLRQQANH PYWADTVKRL LAEGINRPRK GHDAGDHPPI TPMKSATEAE
410 420 430 440 450
LGGDAWRLYE YITRHFIATV SHDCKYLQST ISFRIGPELF TCSGKTVLSP
460 470 480 490 500
GFTEVMPWQS VPLEESLPTC QRGDAFPVGE VKMLEKQTNP PDYLTEAELI
510 520 530 540 550
TLMEKHGIGT DASIPVHINN ICQRNYVTVE SGRRLKPTNL GIVLVHGYYK
560 570 580 590 600
IDAELVLPTI RSAVEKQLNL IAQGKADYRQ VLGHTLDVFK RKFHYFVDSI
610 620 630 640 650
AGMDELMEVS FSPLAATGKP LSRCGKCHRF MKYIQAKPSR LHCSHCDETY
660 670 680 690 700
TLPQNGTIKL YKELRCPLDD FELVLWSSGS RGKSYPLCPY CYNHPPFRDM
710 720 730 740 750
KKGMGCNECT HPSCQHSLSM LGIGQCVECE SGVLVLDPTS GPKWKVACNK
760 770 780 790 800
CNVVAHCFEN AHRVRVSADT CSVCEAALLD VDFNKAKSPL PGDETQHMGC
810 820 830 840 850
VFCDPVFQEL VELKHAASCH PMHRGGPGRR QGRGRGRARR PPGKPNPRRP
860
KDKMSALAAY FV
Length:862
Mass (Da):96,662
Last modified:May 1, 1999 - v1
Checksum:i75532827856CFF8F
GO
Isoform 2 (identifier: O95985-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     703-730: GMGCNECTHPSCQHSLSMLGIGQCVECE → GECSHSLLSTGSCSLFSVPTPALHQAGL
     731-862: Missing.

Show »
Length:730
Mass (Da):82,123
Checksum:i8CC2903C7C4304E6
GO
Isoform 3 (identifier: O95985-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     703-707: GMGCN → VVPCV
     708-862: Missing.

Show »
Length:707
Mass (Da):79,839
Checksum:iBE43F9D46B50AA85
GO

Computationally mapped potential isoform sequencesi

There are 11 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
C9JEI7C9JEI7_HUMAN
DNA topoisomerase
TOP3B
246Annotation score:
H0Y6W0H0Y6W0_HUMAN
DNA topoisomerase
TOP3B
525Annotation score:
H7C4B0H7C4B0_HUMAN
DNA topoisomerase
TOP3B
168Annotation score:
C9JKE2C9JKE2_HUMAN
DNA topoisomerase
TOP3B
121Annotation score:
C9JT00C9JT00_HUMAN
DNA topoisomerase
TOP3B
122Annotation score:
F2Z2A5F2Z2A5_HUMAN
DNA topoisomerase
TOP3B
129Annotation score:
C9J9X4C9J9X4_HUMAN
DNA topoisomerase
TOP3B
61Annotation score:
C9JTQ7C9JTQ7_HUMAN
DNA topoisomerase
TOP3B
42Annotation score:
C9JEQ1C9JEQ1_HUMAN
DNA topoisomerase
TOP3B
60Annotation score:
C9JHR0C9JHR0_HUMAN
DNA topoisomerase
TOP3B
46Annotation score:
There is more potential isoformShow all

Sequence cautioni

The sequence BAA20009 differs from that shown. Reason: Erroneous gene model prediction.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_052591365D → N1 PublicationCorresponds to variant dbSNP:rs9610728Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_006525703 – 730GMGCN…CVECE → GECSHSLLSTGSCSLFSVPT PALHQAGL in isoform 2. CuratedAdd BLAST28
Alternative sequenceiVSP_006527703 – 707GMGCN → VVPCV in isoform 3. Curated5
Alternative sequenceiVSP_006528708 – 862Missing in isoform 3. CuratedAdd BLAST155
Alternative sequenceiVSP_006526731 – 862Missing in isoform 2. CuratedAdd BLAST132

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF053082 mRNA Translation: AAD15791.1
D87012 Genomic DNA Translation: BAA20009.1 Sequence problems.
AF017146 mRNA Translation: AAD01614.1
AF125216 mRNA Translation: AAD29670.1
CR456596 mRNA Translation: CAG30482.1
BC002432 mRNA Translation: AAH02432.1
CCDSiCCDS13797.1 [O95985-1]
RefSeqiNP_001269041.1, NM_001282112.1 [O95985-1]
NP_001269042.1, NM_001282113.1 [O95985-1]
NP_003926.1, NM_003935.4 [O95985-1]
XP_005261868.1, XM_005261811.1 [O95985-1]
XP_006724412.1, XM_006724349.1
XP_006724413.1, XM_006724350.1
XP_011528784.1, XM_011530482.1 [O95985-1]
UniGeneiHs.436401

Genome annotation databases

EnsembliENST00000357179; ENSP00000349705; ENSG00000100038 [O95985-1]
ENST00000398793; ENSP00000381773; ENSG00000100038 [O95985-1]
GeneIDi8940
KEGGihsa:8940
UCSCiuc002zvs.5 human [O95985-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF053082 mRNA Translation: AAD15791.1
D87012 Genomic DNA Translation: BAA20009.1 Sequence problems.
AF017146 mRNA Translation: AAD01614.1
AF125216 mRNA Translation: AAD29670.1
CR456596 mRNA Translation: CAG30482.1
BC002432 mRNA Translation: AAH02432.1
CCDSiCCDS13797.1 [O95985-1]
RefSeqiNP_001269041.1, NM_001282112.1 [O95985-1]
NP_001269042.1, NM_001282113.1 [O95985-1]
NP_003926.1, NM_003935.4 [O95985-1]
XP_005261868.1, XM_005261811.1 [O95985-1]
XP_006724412.1, XM_006724349.1
XP_006724413.1, XM_006724350.1
XP_011528784.1, XM_011530482.1 [O95985-1]
UniGeneiHs.436401

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5GVCX-ray2.44A/B1-612[»]
5GVEX-ray3.61A1-612[»]
ProteinModelPortaliO95985
SMRiO95985
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114452, 38 interactors
ComplexPortaliCPX-1621 TDRD3-TOP3B type IA topoisomerase complex
IntActiO95985, 31 interactors
STRINGi9606.ENSP00000349705

PTM databases

iPTMnetiO95985
PhosphoSitePlusiO95985

Polymorphism and mutation databases

BioMutaiTOP3B

Proteomic databases

EPDiO95985
MaxQBiO95985
PaxDbiO95985
PeptideAtlasiO95985
PRIDEiO95985
ProteomicsDBi51161
51162 [O95985-2]
51163 [O95985-3]

Protocols and materials databases

DNASUi8940
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000357179; ENSP00000349705; ENSG00000100038 [O95985-1]
ENST00000398793; ENSP00000381773; ENSG00000100038 [O95985-1]
GeneIDi8940
KEGGihsa:8940
UCSCiuc002zvs.5 human [O95985-1]

Organism-specific databases

CTDi8940
DisGeNETi8940
EuPathDBiHostDB:ENSG00000100038.19
GeneCardsiTOP3B
HGNCiHGNC:11993 TOP3B
HPAiHPA069678
MIMi603582 gene
neXtProtiNX_O95985
OpenTargetsiENSG00000100038
PharmGKBiPA36674
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1956 Eukaryota
COG0550 LUCA
GeneTreeiENSGT00530000063430
HOGENOMiHOG000184378
HOVERGENiHBG059857
InParanoidiO95985
KOiK03165
OMAiTYPRVDT
OrthoDBiEOG091G01EW
PhylomeDBiO95985
TreeFamiTF105288

Miscellaneous databases

ChiTaRSiTOP3B human
GeneWikiiTOP3B
GenomeRNAii8940
PROiPR:O95985
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000100038 Expressed in 120 organ(s), highest expression level in dorsal plus ventral thalamus
CleanExiHS_TOP3B
ExpressionAtlasiO95985 baseline and differential
GenevisibleiO95985 HS

Family and domain databases

CDDicd00186 TOP1Ac, 1 hit
cd03362 TOPRIM_TopoIA_TopoIII, 1 hit
Gene3Di1.10.290.10, 1 hit
1.10.460.10, 1 hit
2.70.20.10, 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
IPR006171 TOPRIM_domain
IPR034144 TOPRIM_TopoIII
PANTHERiPTHR11390 PTHR11390, 1 hit
PfamiView protein in Pfam
PF01131 Topoisom_bac, 1 hit
PF01751 Toprim, 1 hit
PRINTSiPR00417 PRTPISMRASEI
SMARTiView protein in SMART
SM00437 TOP1Ac, 1 hit
SM00436 TOP1Bc, 1 hit
SM00493 TOPRIM, 1 hit
SUPFAMiSSF56712 SSF56712, 1 hit
PROSITEiView protein in PROSITE
PS00396 TOPOISOMERASE_I_PROK, 1 hit
PS50880 TOPRIM, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiTOP3B_HUMAN
AccessioniPrimary (citable) accession number: O95985
Secondary accession number(s): A0M8Q3, Q9BUP5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 1, 1999
Last modified: November 7, 2018
This is version 173 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. Human chromosome 22
    Human chromosome 22: entries, gene names and cross-references to MIM
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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