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Protein Overview: TDP1

General Information:
Name(s) found: TDP1 / YBR223C [SGD]
Description(s) found:
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  • gi|6319701|ref|NP_009782.1| Tyrosyl-DNA Phosphodiesterase I, hydrolyzes 3'-phosphotyrosyl bonds to generate 3'-phosphate DNA and tyrosine, involved in the repair of DNA lesions created by topoisomerase I; Tdp1p [Saccharomyces cerevisiae] [NCBI NR]
  • pir||S46099 hypothetical protein YBR223c - yeast (Saccharomyces cerevisiae) [NCBI NR]
  • gi|586340|sp|P38319.1|TYDP1_YEAST RecName: Full=Tyrosyl-DNA phosphodiesterase 1; Short=Tyr-DNA phosphodiesterase 1 [NCBI NR]
  • gi|55669557|pdb|1Q32|D Chain D, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna Phosphodiesterase [NCBI NR]
  • gi|55669556|pdb|1Q32|C Chain C, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna Phosphodiesterase [NCBI NR]
  • gi|55669555|pdb|1Q32|B Chain B, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna Phosphodiesterase [NCBI NR]
  • gi|55669554|pdb|1Q32|A Chain A, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna Phosphodiesterase [NCBI NR]
  • gi|536617|emb|CAA85186.1| unnamed protein product [Saccharomyces cerevisiae] [NCBI NR]
  • (P38319) Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) (Tyr-DNA phosphodiesterase 1) [Swiss-Prot]
  • Tyrosyl-DNA phosphodiesterase 1 OS=Saccharomyces cerevisiae GN=TDP1 PE=1 SV=1 [Swiss-Prot]
  • TDP1 Tyr-DNA phosphodiesterase [mips]
  • Tyrosyl-DNA Phosphodiesterase I, hydrolyzes 3' and 5'-phosphotyrosyl bonds, involved in the repair of DNA lesions created by topoisomerase I and topoisomerase II; mutations in human homolog result in the neurodegenerative disease SCANI [SGD]
  • YBR223C, Chr II from 668621-670255, reverse complement [yeast_orfs2]
  • Chr II from 668621-670255, reverse complement [yeastorf3.fasta]
  • Chr II from 668620-670254, reverse complement [yeastorf4.fasta]
  • Chr II from 670252-668618, reverse complement [yeastorf5.fasta]
  • TDP1 SGDID:S0000427, Chr II from 670254-668620, reverse complement, Verified ORF [yeastflysequest.fasta]
  • TDP1 SGDID:S0000427, Chr II from 670292-668658, reverse complement, Verified ORF [10112005cervSGD.fasta]
  • Tdp1p [Saccharomyces cerevisiae]gi|536617|emb|CAA85186.1| unnamed protein product [Saccharomyces cerevisiae]gi|586340|sp|P38319|TYDP_YEAST Tyrosyl-DNA phosphodiesterase 1 (Tyr-DNA phosphodiesterase 1)gi|626545|pir||S46099 hypothetical protein YBR223c - [nrdb_11152004_Chlamydomonas]
  • TDP1 SGDID:S000000427, Chr II from 670292-668658, reverse complement, Verified ORF, "Tyrosyl-DNA Phosphodiesterase I, hydrolyzes 3'-phosphotyrosyl bonds to generate 3'-phosphate DNA and tyrosine, involved in the repair of DNA lesions created by topoisomer [SGD_S-cerevisiae_na_12-16-2005_con_reversed.fasta]
  • TDP1 SGDID:S000000427, Chr II from 670292-668658, reverse complement, Verified ORF, "Tyrosyl-DNA Phosphodiesterase I, hydrolyzes 3' and 5'-phosphotyrosyl bonds, involved in the repair of DNA lesions created by topoisomerase I and topoisomerase II; mutatio [yeast-200209-contam.fasta]
  • unnamed protein product [Saccharomyces cerevisiae] [nr-271106-contam.fasta]
  • Tyrosyl-DNA Phosphodiesterase I, hydrolyzes 3'-phosphotyrosyl bonds to generate 3'-phosphate DNA and tyrosine, involved in the repair of DNA lesions created by topoisomerase I; Tdp1p [Saccharomyces cerevisiae] [nr-271106-contam.fasta]
  • Chain C, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna Phosphodiesterase [nr-271106-contam.fasta]
  • Chain D, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna Phosphodiesterase [nr-271106-contam.fasta]
  • Chain A, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna Phosphodiesterase [nr-271106-contam.fasta]
  • Tyrosyl-DNA phosphodiesterase 1 (Tyr-DNA phosphodiesterase 1) [nr-271106-contam.fasta]
  • Chain B, Crystal Structure Analysis Of The Yeast Tyrosyl-Dna Phosphodiesterase [nr-271106-contam.fasta]
  • TDP1 SGDID:S000000427, Chr II from 670292-668658, reverse complement, Verified ORF, "Tyrosyl-DNA Phosphodiesterase I, hydrolyzes 3' and 5'-phosphotyrosyl bonds, involved in the repair of DNA lesions created by topoisomerase I and topoisomerase II; mutations in human homolog result in the neurodegenerative disease SCANI" [yeast-bovrabprots.fasta]
  • TDP1 SGDID:S000000427, Chr II from 670292-668658, reverse complement, Verified ORF, "Tyrosyl-DNA Phosphodiesterase I, hydrolyzes 3'-phosphotyrosyl bonds to generate 3'-phosphate DNA and tyrosine, involved in the repair of DNA lesions created by topoisomerase I" [yeast-contam_custom.fasta]
  • [chemostatdb.fasta]
  • Tyrosyl-DNA phosphodiesterase 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TDP1 PE=1 SV=1 [UniProt_S_cerevisiae_20120516_05-16-2012_reversed.fasta]
  • TDP1 SGDID:S000000427, Chr II from 670297-668663, Genome Release 64-1-1, reverse complement, Verified ORF, "Tyrosyl-DNA Phosphodiesterase I, hydrolyzes 3' and 5'-phosphotyrosyl bonds, involved in the repair of DNA lesions created by topoisomerase I and topoisomerase II; mutations in human homolog result in the neurodegenerative disease SCANI" [yeast-030211-contam.fasta]
  • TDP1 SGDID:S000000427, Chr II from 670297-668663, Genome Release 64-2-1, reverse complement, Verified ORF, "Tyrosyl-DNA phosphodiesterase I; hydrolyzes 3' and 5'-phosphotyrosyl bonds; involved in the repair of DNA lesions created by topoisomerase I and topoisomerase II; mutations in human homolog result in the neurodegenerative disease SCANI" [20141208_orf_trans.fasta]
  • TR514|c0_g1_i1|g.288 ORF TR514|c0_g1_i1|g.288 TR514|c0_g1_i1|m.288 type:complete len:545 (+) TR514|c0_g1_i1:300-1934(+) [Y12_S_cerevisiae-Sep2015-contam.fasta]
  • YBR223C SGDID:S000000427, Chr II from 670297-668663, Genome Release 64-1-1, reverse complement, Verified ORF, "Tyrosyl-DNA Phosphodiesterase I, hydrolyzes 3' and 5'-phosphotyrosyl bonds, involved in the repair of DNA lesions created by topoisomerase I and topoisomerase II; mutations in human homolog result in the neurodegenerative disease SCANI" [2016-01-SGD_Yeast_Contam_Riffle_20140507-Ska-Hec-110-tubulin.fasta]
  • asmbl_5125|g.3763 ORF asmbl_5125|g.3763 asmbl_5125|m.3763 type:complete len:545 (+) asmbl_5125:299-1933(+) [Y12_Trinity_v2_2_0_PASA_6May2016-contam.fasta]
  • ID=asmbl_5129|g.3089 ORF ID=asmbl_5129|g.3089 ID=asmbl_5129|m.3089 type:complete len:545 (+) ID=asmbl_5129:300-1934(+) [Y12_quiver_Trinity_v2_2_0_PASA_2June2016-contam.fasta]
    • Organism: Saccharomyces cerevisiae
    Length: 544 amino acids

    Gene Ontology:
    Cellular Component: nucleus [IDALink to PubMed article][IMPLink to PubMed article]
    Biological Process: DNA repair [IMPLink to PubMed article]
    Molecular Function: 3'-tyrosyl-DNA phosphodiesterase activity [IDALink to PubMed article]


    Sequence:
    Sequence:
    [PDR BLAST]
    [ProtParam] 
          1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSRETNFNGT KRKRSDVAEK VAQRWKSVRY SAEMENMAPV NSNNDSDDCV IVSESKIIDL  60
   61 TNQEQDLSER IETNDTAKGA VFKLMKSDFY EREDFMGEVE DMITLKDIFG TETLKRSILF 120
  121 SFQYELDFLL RQFHQNVENI TIVGQKGTIM PIEARAMDAT LAVILKKVKL IEITMPPFAS 180
  181 HHTKLIINFY DNGECKIFLP SNNFTSMETN LPQQVCWCSP LLKIGKEGLP VPFKRSLIEY 240
  241 LNSYHLKDID ELITKSVEEV NFAPLSELEF VYSTPSKFQS SGLLSFYNKL EKLSAGTSAS 300
  301 DTAKHYLCQT SSIGTSLSRA RDENLWTHLM IPLFTGIMSP PAKDTAGRKK AEILPTNSLI 360
  361 NEYSQRKIKP YIIFPTEQEF VTSPLKWSSS GWFHFQYLQK KSYYEMLRNK FKVFYKQDPA 420
  421 MVTRRRGTTP AHSKFYMHCA TNSAGPCDAS QVFKELEWCL YTSANLSQTA WGTVSRKPRN 480
  481 YEAGVLYHSR RLANTRKVTC RTFTRDRRGC AGNPTHVAVP FTLPVIPYDL AEDECFCLAR 540
  541 HEND

    Protein Complex Data

      PUBLICATION TOPOLOGY COCOMPLEXED PROTEINS
    View Details Krogan NJ, et al. (2006) TDP1 YGL082W
    View Details Ho Y, et al. (2002) RNQ1 SHP1 TDP1

    Mass Spectrometry Data

    No mass spectrometry results found for this protein.

    Yeast Two-Hybrid Data

    The following interactions contain this protein:

    NOT SHOWING SINGLE HITS. [ Show Single Hits ]

    [View our yeast two-hybrid interpretation guidelines.]

    No yeast two-hybrid interactions found for this protein.

    Microscopy / Localization Data

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      PROTEIN(S) PUBLICATION
    View Data TDP1 Huh WK, et al. (2003)

    Protein Structure Data


    [What does the above image mean?]
    [View Top Sequence Alignments] [Show Ginzu Version Information]

    Domains predicted:

    #   Region(s) Method Confidence Match Description
    1 View Details [1..222] PSI-BLAST 289.9897 Tyrosyl-DNA phosphodiesterase TDP1
    2 View Details [223..268] PSI-BLAST 289.9897 Tyrosyl-DNA phosphodiesterase TDP1
    3 View Details [269..287]
    [461..486]    		 PSI-BLAST 289.9897 Tyrosyl-DNA phosphodiesterase TDP1
    4 View Details [288..460]
    [487..544]    		 PSI-BLAST 289.9897 Tyrosyl-DNA phosphodiesterase TDP1

    Functions predicted (by domain):

    # Gene Ontology predictions
    1
    Term Confidence Notes
  • 3'-tyrosyl-DNA phosphodiesterase activity
    		•  1.46693175347055 bayes_pls_golite062009
  • tyrosyl-DNA phosphodiesterase activity
    		•  1.46693175347055 bayes_pls_golite062009
  • structure-specific DNA binding
    		•  1.41591686174898 bayes_pls_golite062009
  • double-stranded DNA binding
    		•  1.29668490323599 bayes_pls_golite062009
  • single-stranded DNA binding
    		•  1.29429720882252 bayes_pls_golite062009
  • catalytic activity
    		•  1.29236214516383 bayes_pls_golite062009
  • binding
    		•  1.26667168593698 bayes_pls_golite062009
  • nucleic acid binding
    		•  0.926017334343152 bayes_pls_golite062009
  • DNA binding
    		•  0.840595330626189 bayes_pls_golite062009
  • transferase activity, transferring phosphorus-containing groups
    		•  0.235198647671849 bayes_pls_golite062009
  • protein binding
    		•  0.162885453822356 bayes_pls_golite062009
    2 No functions predicted.
    3 No functions predicted.
    4 No functions predicted.


    Reference: Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076


    Philius Transmembrane Prediction:

    Protein predicted to be: GLOBULAR (No transmembrane regions or signal peptide)
    Confidence of classification: 0.99

    Source: Reynolds et al. (2008)

    YRC Informatics Platform - Version 3.0
    Created and Maintained by: Michael Riffle