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Protein

DNA topoisomerase 3-beta-1

Gene

TOP3B

Organism
Homo sapiens (Human)
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 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)LengthDescriptionGraphical viewFeature identifierActions
Active sitei336 – 3361O-(5'-phospho-DNA)-tyrosine intermediateBy similarity

GO - Molecular functioni

  • DNA binding Source: ProtInc
  • DNA topoisomerase activity Source: ProtInc
  • DNA topoisomerase type I activity Source: UniProtKB-EC
  • poly(A) RNA binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding

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
ProteomesiUP000005640 Componenti: Chromosome 22

Organism-specific databases

HGNCiHGNC:11993. TOP3B.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA36674.

Polymorphism and mutation databases

BioMutaiTOP3B.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 862862DNA topoisomerase 3-beta-1PRO_0000145192Add
BLAST

Proteomic databases

MaxQBiO95985.
PaxDbiO95985.
PRIDEiO95985.

PTM databases

PhosphoSiteiO95985.

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

BgeeiO95985.
CleanExiHS_TOP3B.
ExpressionAtlasiO95985. baseline and differential.
GenevisibleiO95985. HS.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
ADAMTSL4Q6UY14-33EBI-373403,EBI-10173507
MID2Q9UJV3-23EBI-373403,EBI-10172526
PNMA2Q9UL423EBI-373403,EBI-302355
SPRED2Q7Z6983EBI-373403,EBI-7082156
SSX2IPQ9Y2D83EBI-373403,EBI-2212028
TRIM41Q8WV443EBI-373403,EBI-725997

Protein-protein interaction databases

BioGridi114452. 22 interactions.
IntActiO95985. 10 interactions.
MINTiMINT-1458306.
STRINGi9606.ENSP00000349705.

Structurei

3D structure databases

ProteinModelPortaliO95985.
SMRiO95985. Positions 5-633.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 153151ToprimPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0550.
GeneTreeiENSGT00530000063430.
HOGENOMiHOG000184378.
HOVERGENiHBG059857.
InParanoidiO95985.
KOiK03165.
OMAiGLIARQY.
OrthoDBiEOG7RBZ7N.
PhylomeDBiO95985.
TreeFamiTF105288.

Family and domain databases

Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 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.
IPR013825. Topo_IA_cen_sub2.
IPR023405. Topo_IA_core_domain.
IPR003602. Topo_IA_DNA-bd_dom.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

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

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

Sequence cautioni

The sequence BAA20009.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti365 – 3651D → N.1 Publication
Corresponds to variant rs9610728 [ dbSNP | Ensembl ].
VAR_052591

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei703 – 73028GMGCN…CVECE → GECSHSLLSTGSCSLFSVPT PALHQAGL in isoform 2. CuratedVSP_006525Add
BLAST
Alternative sequencei703 – 7075GMGCN → VVPCV in isoform 3. CuratedVSP_006527
Alternative sequencei708 – 862155Missing in isoform 3. CuratedVSP_006528Add
BLAST
Alternative sequencei731 – 862132Missing in isoform 2. CuratedVSP_006526Add
BLAST

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. [O95985-1]
XP_006724413.1. XM_006724350.1. [O95985-1]
UniGeneiHs.436401.

Genome annotation databases

EnsembliENST00000357179; ENSP00000349705; ENSG00000100038. [O95985-1]
ENST00000398793; ENSP00000381773; ENSG00000100038. [O95985-1]
GeneIDi8940.
KEGGihsa:8940.
UCSCiuc002zvs.3. human. [O95985-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

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. [O95985-1]
XP_006724413.1. XM_006724350.1. [O95985-1]
UniGeneiHs.436401.

3D structure databases

ProteinModelPortaliO95985.
SMRiO95985. Positions 5-633.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114452. 22 interactions.
IntActiO95985. 10 interactions.
MINTiMINT-1458306.
STRINGi9606.ENSP00000349705.

PTM databases

PhosphoSiteiO95985.

Polymorphism and mutation databases

BioMutaiTOP3B.

Proteomic databases

MaxQBiO95985.
PaxDbiO95985.
PRIDEiO95985.

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.3. human. [O95985-1]

Organism-specific databases

CTDi8940.
GeneCardsiGC22M022309.
HGNCiHGNC:11993. TOP3B.
MIMi603582. gene.
neXtProtiNX_O95985.
PharmGKBiPA36674.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG0550.
GeneTreeiENSGT00530000063430.
HOGENOMiHOG000184378.
HOVERGENiHBG059857.
InParanoidiO95985.
KOiK03165.
OMAiGLIARQY.
OrthoDBiEOG7RBZ7N.
PhylomeDBiO95985.
TreeFamiTF105288.

Miscellaneous databases

GeneWikiiTOP3B.
GenomeRNAii8940.
NextBioi33622.
PROiO95985.
SOURCEiSearch...

Gene expression databases

BgeeiO95985.
CleanExiHS_TOP3B.
ExpressionAtlasiO95985. baseline and differential.
GenevisibleiO95985. HS.

Family and domain databases

Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 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.
IPR013825. Topo_IA_cen_sub2.
IPR023405. Topo_IA_core_domain.
IPR003602. Topo_IA_DNA-bd_dom.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A new human topoisomerase III that interacts with SGS1 protein."
    Ng S.-W., Liu Y., Hasselblatt K.T., Mok S.C., Berkowitz R.S.
    Nucleic Acids Res. 27:993-1000(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), ALTERNATIVE SPLICING, TISSUE SPECIFICITY.
  2. "One-megabase sequence analysis of the human immunoglobulin lambda gene locus."
    Kawasaki K., Minoshima S., Nakato E., Shibuya K., Shintani A., Schmeits J.L., Wang J., Shimizu N.
    Genome Res. 7:250-261(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. Hanai R., Li W., Wang J.C.
    Submitted (AUG-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  4. Riou J.F., Goulaouic H., Grondard L.
    Submitted (FEB-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
  6. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT ASN-365.
    Tissue: Skin.

Entry informationi

Entry nameiTOP3B_HUMAN
AccessioniPrimary (citable) accession number: O95985
Secondary accession number(s): A0M8Q3, Q9BUP5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 1, 1999
Last modified: June 24, 2015
This is version 143 of the entry and version 1 of the sequence. [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

Complete proteome, Reference proteome

Documents

  1. Human chromosome 22
    Human chromosome 22: entries, gene names and cross-references to MIM
  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. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.