CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-012114
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 DNA topoisomerase 3-alpha 
Protein Synonyms/Alias
 DNA topoisomerase III alpha 
Gene Name
 TOP3A 
Gene Synonyms/Alias
 TOP3 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
35MALRGVRKVLCVAEKubiquitination[1]
42KVLCVAEKNDAAKGIubiquitination[1]
47AEKNDAAKGIADLLSubiquitination[1]
168IHVCKAVKPNLQVLRubiquitination[1]
257GFVVERFKAIQAFVPubiquitination[1, 2, 3]
321VRSKPKSKWRPQALDubiquitination[1]
334LDTVELEKLASRKLRubiquitination[1]
345RKLRINAKETMRIAEubiquitination[1]
353ETMRIAEKLYTQGYIubiquitination[1]
421HPPIHPTKYTNNLQGubiquitination[1]
546AEHIETIKARMYVGLubiquitination[1]
557YVGLTPDKRFLPGHLubiquitination[1]
602ICDGKKDKFVVLRQQubiquitination[1]
671DMVLKTKKNGGFYLSubiquitination[1]
Reference
 [1] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [2] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [3] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789] 
Functional Description
 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 processing of homologous recombination intermediates to limit DNA crossover formation in cells. Has DNA decatenation activity. 
Sequence Annotation
 DOMAIN 35 179 Toprim.
 REPEAT 812 839 1.
 REPEAT 896 923 2.
 ZN_FING 658 685 C4-type (Potential).
 REGION 812 923 2 X 27 AA approximate repeats.
 ACT_SITE 362 362 O-(5'-phospho-DNA)-tyrosine intermediate  
Keyword
 Alternative splicing; ATP-binding; Complete proteome; DNA-binding; Isomerase; Magnesium; Metal-binding; Nucleotide-binding; Polymorphism; Reference proteome; Repeat; Topoisomerase; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1001 AA 
Protein Sequence
MIFPVARYAL RWLRRPEDRA FSRAAMEMAL RGVRKVLCVA EKNDAAKGIA DLLSNGRMRR 60
REGLSKFNKI YEFDYHLYGQ NVTMVMTSVS GHLLAHDFQM QFRKWQSCNP LVLFEAEIEK 120
YCPENFVDIK KTLERETRQC QALVIWTDCD REGENIGFEI IHVCKAVKPN LQVLRARFSE 180
ITPHAVRTAC ENLTEPDQRV SDAVDVRQEL DLRIGAAFTR FQTLRLQRIF PEVLAEQLIS 240
YGSCQFPTLG FVVERFKAIQ AFVPEIFHRI KVTHDHKDGI VEFNWKRHRL FNHTACLVLY 300
QLCVEDPMAT VVEVRSKPKS KWRPQALDTV ELEKLASRKL RINAKETMRI AEKLYTQGYI 360
SYPRTETNIF PRDLNLTVLV EQQTPDPRWG AFAQSILERG GPTPRNGNKS DQAHPPIHPT 420
KYTNNLQGDE QRLYEFIVRH FLACCSQDAQ GQETTVEIDI AQERFVAHGL MILARNYLDV 480
YPYDHWSDKI LPVYEQGSHF QPSTVEMVDG ETSPPKLLTE ADLIALMEKH GIGTDATHAE 540
HIETIKARMY VGLTPDKRFL PGHLGMGLVE GYDSMGYEMS KPDLRAELEA DLKLICDGKK 600
DKFVVLRQQV QKYKQVFIEA VAKAKKLDEA LAQYFGNGTE LAQQEDIYPA MPEPIRKCPQ 660
CNKDMVLKTK KNGGFYLSCM GFPECRSAVW LPDSVLEASR DSSVCPVCQP HPVYRLKLKF 720
KRGSLPPTMP LEFVCCIGGC DDTLREILDL RFSGGPPRAS QPSGRLQANQ SLNRMDNSQH 780
PQPADSRQTG SSKALAQTLP PPTAAGESNS VTCNCGQEAV LLTVRKEGPN RGRQFFKCNG 840
GSCNFFLWAD SPNPGAGGPP ALAYRPLGAS LGCPPGPGIH LGGFGNPGDG SGSGTSCLCS 900
QPSVTRTVQK DGPNKGRQFH TCAKPREQQC GFFQWVDENT APGTSGAPSW TGDRGRTLES 960
EARSKRPRAS SSDMGSTAKK PRKCSLCHQP GHTRPFCPQN R 1001 
Gene Ontology
 GO:0005694; C:chromosome; IEA:InterPro.
 GO:0016605; C:PML body; IDA:UniProtKB.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0003917; F:DNA topoisomerase type I activity; IDA:UniProtKB.
 GO:0008270; F:zinc ion binding; IEA:InterPro.
 GO:0006265; P:DNA topological change; IDA:UniProtKB.
 GO:0007126; P:meiosis; TAS:ProtInc. 
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.
 IPR023405; Topo_IA_core_domain.
 IPR003602; Topo_IA_DNA-bd.
 IPR013498; Topo_IA_Znf.
 IPR006171; Toprim_domain.
 IPR001878; Znf_CCHC.
 IPR010666; Znf_GRF. 
Pfam
 PF01131; Topoisom_bac
 PF01751; Toprim
 PF01396; zf-C4_Topoisom
 PF06839; zf-GRF 
SMART
 SM00437; TOP1Ac
 SM00436; TOP1Bc
 SM00493; TOPRIM
 SM00343; ZnF_C2HC 
PROSITE
 PS00396; TOPOISOMERASE_I_PROK
 PS50880; TOPRIM 
PRINTS
 PR00417; PRTPISMRASEI.