TDT BOVIN

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Author Information

Cynthia Hao

Basic Information

  • ID: TDT_BOVIN
  • Name: DNTT
  • Organism: Bos taurus (Bovine)
  • UniProt ID: [1]
  • Description: This gene codes for DNA nucleotidylexotransferase, also known as terminal deoxynucleotidyl transferase (TdT). [2] TdT is a DNA polymerase in the type X family that can add bases to the 3' end of DNA without a complementary template strand. [3] TdT adds bases randomly to a starting strand of at least 3 nucleotides, preferentially adding guanine and cytosine and avoiding adenine. [4] TdT activity is actually inhibited by ribonucleotides and will not add as well to an RNA primer or RNA bases. [5] The enzyme uses divalent cations like Mg2+, Co2+, Zn2+ and Mn2+ to catalyze the addition of a deoxynucleoside triphosphate (dNTP) to DNA, resulting in release of a pyrophosphate and addition of the nucleotide. [6] Depending on which cofactor cation is used, TdT will prefer different dNTPs. [7] Template-independent polymerase activity is important in the immune system for generating random antibody DNA sequences for B and T cells that can recognize foreign DNA. [8] TdT works with two other polymerases in the type X family, pol μ and pol λ, to perform this function. [9]. Another function of TdT is adding random bases to cut DNA strands to assist in DNA repair via non-homologous end joining.[10] TdT most likely adds distributively, separating from each DNA strand and binding to a new one each time it adds a base, and it binds to its two substrates in random order, unlike normal polymerases that must bind the longer DNA first. So far, TdT has been characterized in mice, bovines, and humans. Bovine TdT has 3 splice variants—two long variants with exonuclease ability and one short variant without it. [11]. TdT is challenging to produce in bacteria because of codon bias mismatches between bacteria and eukaryotic cells, and enzyme that is produced is typically less effective and less able to be incorporated into E. coli cells. [12]
  • DNA Length: 1527 base pairs.
  • DNA sequence (from Bos taurus gene found with BLAST search of amino acid sequence):

CTCCCTCTCTTCTGGAGATACCACTTGATGGCACAGCCAGAGGCAGCATCAGCGTCTTCCCATGGATCCG CTGTGCACAGCCTCCTCAGGCCCTCGGAAGAAGAGACCCAGGCAGGTGGGTGCCTCAATGGCCTCCCCTC CTCATGACATCAAGTTTCAAAATTTGGTCCTCTTCATTTTGGAGAAGAAAATGGGAACCACCCGCAGAAA CTTCCTCATGGAGCTGGCTCGAAGGAAAGGTTTCAGGGTTGAAAATGAGCTCAGTGATTCTGTCACCCAC ATTGTAGCAGAAAACAACTCTGGTTCAGAGGTTCTCGAGTGGCTTCAGGTACAGAACATAAGAGCCAGCT CGCAGCTAGAACTCCTTGATGTCTCCTGGCTGATCGAAAGTATGGGAGCAGGAAAACCAGTGGAGATTAC AGGAAAACACCAGCTTGTTGTGAGAACAGACTATTCAGCTACCCCAAACCCAGGCTTCCAGAAGACTCCA CCACTTGCTGTAAAAAAGATCTCCCAGTACGCGTGTCAAAGAAAAACCACTTTGAACAACTATAACCACA TATTCACGGATGCCTTTGAGATACTGGCTGAAAATTCTGAGTTTAAAGAAAATGAAGTCTCTTATGTGAC ATTTATGAGAGCAGCTTCTGTACTTAAATCTCTGCCATTCACAATCATCAGTATGAAGGATACAGAAGGA ATTCCCTGCCTGGGGGACAAGGTGAAGTGTATCATAGAGGAAATTATTGAAGATGGAGAAAGTTCTGAAG TTAAAGCTGTGTTAAATGATGAACGATATCAGTCCTTCAAACTCTTTACTTCTGTTTTTGGAGTGGGACT GAAGACATCTGAGAAATGGTTCAGGATGGGGTTCAGATCTCTGAGTAAAATAATGTCAGACAAAACCCTG AAATTCACAAAAATGCAGAAAGCAGGATTTCTCTATTATGAAGACCTTGTCAGCTGCGTGACCAGGGCCG AAGCAGAGGCGGTTGGCGTGCTGGTTAAAGAGGCTGTGTGGGCATTTCTGCCGGATGCCTTTGTCACCAT GACAGGAGGATTCCGCAGGGGTAAGAAGATTGGGCATGATGTAGATTTTTTAATTACCAGTCCAGGATCA GCAGAGGATGAAGAGCAACTTTTGCCTAAAGTGATAAACTTATGGGAAAAAAAGGGATTACTTTTATATT ATGACCTTGTGGAGTCAACATTTGAAAAGTTCAAGTTGCCAAGCAGGCAGGTGGATACTTTAGATCATTT TCAAAAATGCTTTCTGATTTTAAAATTGCACCATCAGAGAGTAGACAGTAGCAAGTCCAACCAGCAGGAA GGAAAGACCTGGAAGGCCATCCGTGTGGACCTGGTTATGTGCCCCTACGAGAACCGTGCCTTTGCCCTGC TAGGCTGGACTGGCTCCCGGCAGTTTGAGAGAGACATCCGGCGCTATGCCACACACGAGCGGAAGATGAT GCTGGATAACCACGCTTTATATGACAAGACCAAGAGGGTATTTCTCAAAGCGGAAAGTGAAGAAGAAATC TTTGCACATCTGGGATTGGACTACATTGAACCATGGGAAAGAAATGCTTAGGAGAAAGCTGTCAACTTTT TTCTTTTCTGTTCTTTTTTTCAGGTTAGACAAATTATGCTTCATATTATCATGAAAGATGCCTTAGTCAA GTTTGGGATTCTTTACATTTTACCAAGATGTAGATTGCTTCTAGAAATAAGTAGTTTTGGAAACGTGATC AGGCACCCCCTGGGTTATGCTCTGGCAAGCCATTTGCAGGACTGATGTGTAGAACTCGCAATGCATTTTC CATAGAAACAGTGTTGGAATTGGTGGCTCATTTCCAGGGAAGTTCATCAAAGCCCACTTTGCCCACAGTG TAGCTGAAATACTGTATACTTCCAATAAAAATAGGAAAAAACAA XM_005225429.2

  • DNA sequence (codon optimized for E. coli):

ATG GAC CCT TTG TGT ACT GCG AGC AGC GGT CCA CGT AAA AAA CGC CCA CGT CAG GTC GGC GCG TCT ATG GCG TCG CCT CCG CAC GAC ATT AAA TTT CAG AAC CTG GTC CTT TTC ATC TTG GAA AAG AAG ATG GGA ACC ACC CGT CGC AAC TTT CTT ATG GAA TTA GCT CGC CGC AAA GGA TTC CGC GTT GAA AAT GAA TTG TCG GAC AGT GTC ACC CAC ATC GTA GCG GAA AAC AAC AGC GGT TCA GAG GTC TTG GAG TGG CTT CAA GTT CAG AAT ATT CGT GCG AGC AGT CAA TTA GAA TTG CTT GAC GTC AGT TGG CTT ATT GAG AGC ATG GGG GCT GGT AAA CCG GTC GAG ATT ACG GGT AAG CAC CAA CTG GTG GTG CGC ACA GAC TAC AGT GCA ACC CCT AAT CCA GGC TTT CAG AAG ACA CCG CCA CTT GCA GTA AAG AAG ATC AGT CAA TAT GCT TGT CAA CGC AAA ACG ACG CTG AAT AAC TAC AAC CAT ATT TTC ACA GAC GCA TTT GAG ATC TTG GCC GAG AAT AGT GAG TTT AAA GAA AAT GAA GTA TCA TAC GTG ACT TTT ATG CGT GCA GCC TCC GTC CTG AAA TCT TTA CCG TTC ACA ATT ATT TCG ATG AAA GAC ACG GAA GGA ATC CCG TGT TTA GGT GAC AAG GTC AAA TGC ATT ATT GAA GAG ATC ATC GAG GAC GGT GAG TCC TCG GAA GTC AAA GCC GTA TTA AAC GAC GAG CGC TAC CAA AGC TTC AAG TTA TTT ACG AGT GTG TTC GGG GTT GGA CTG AAG ACG TCA GAA AAA TGG TTC CGT ATG GGG TTT CGC AGC CTT AGC AAA ATC ATG AGC GAC AAG ACG TTA AAA TTT ACG AAG ATG CAA AAA GCC GGT TTC CTG TAT TAT GAG GAT TTG GTT AGC TGT GTC ACT CGT GCC GAA GCA GAA GCT GTG GGC GTG CTT GTT AAA GAA GCC GTA TGG GCG TTC CTG CCG GAC GCA TTT GTA ACG ATG ACG GGG GGC TTC CGC CGT GGG AAG AAG ATT GGC CAT GAC GTA GAT TTT TTA ATC ACA TCG CCC GGA AGC GCT GAA GAC GAG GAG CAA CTG CTG CCT AAA GTT ATT AAC CTT TGG GAG AAA AAA GGA TTG CTT TTG TAC TAT GAT CTT GTT GAA TCA ACC TTT GAA AAG TTC AAA TTA CCC TCA CGC CAA GTC GAC ACT CTG GAT CAC TTT CAG AAG TGC TTT CTT ATT CTT AAA CTG CAC CAT CAG CGT GTC GAC AGT TCA AAG TCG AAC CAA CAA GAA GGA AAA ACC TGG AAA GCT ATT CGT GTA GAC CTT GTG ATG TGC CCA TAT GAG AAC CGC GCG TTC GCC CTG TTA GGC TGG ACG GGC TCG CGT CAG TTT GAG CGT GAC ATT CGT CGT TAC GCC ACC CAT GAG CGT AAG ATG ATG TTA GAC AAT CAC GCC CTG TAC GAT AAA ACA AAG CGT GTT TTC CTG AAA GCT GAG TCA GAG GAA GAG ATT TTT GCG CAT CTG GGG TTG GAC TAC ATT GAG CCG TGG GAA CGT AAC GCT TAA

  • Amino Acid length: 509 amino acids.
  • Amino Acid sequence:

MDPLCTASSGPRKKRPRQVGASMASPPHDIKFQNLVLFILEKKMGTTRRNFLMELARRKG FRVENELSDSVTHIVAENNSGSEVLEWLQVQNIRASSQLELLDVSWLIESMGAGKPVEIT GKHQLVVRTDYSATPNPGFQKTPPLAVKKISQYACQRKTTLNNYNHIFTDAFEILAENSE FKENEVSYVTFMRAASVLKSLPFTIISMKDTEGIPCLGDKVKCIIEEIIEDGESSEVKAV LNDERYQSFKLFTSVFGVGLKTSEKWFRMGFRSLSKIMSDKTLKFTKMQKAGFLYYEDLV SCVTRAEAEAVGVLVKEAVWAFLPDAFVTMTGGFRRGKKIGHDVDFLITSPGSAEDEEQL LPKVINLWEKKGLLLYYDLVESTFEKFKLPSRQVDTLDHFQKCFLILKLHHQRVDSSKSN QQEGKTWKAIRVDLVMCPYENRAFALLGWTGSRQFERDIRRYATHERKMMLDNHALYDKT KRVFLKAESEEEIFAHLGLDYIEPWERNA

Function and Homologs

  • Product: Terminal deoxynucleotidyl transferase
  • Module: Terminal deoxynucleotidyl transferase
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • Bison bison bison DNA nucleotidylexotransferase (DNTT), transcript variant X1, mRNA, Max score: 1044, Query cover: 100%, E-Value: 0.0, Ident: 99%, Accession number: XM_010833030.1 [13]
    • Bos indicus DNA nucleotidylexotransferase (DNTT), transcript variant X1, mRNA, Max score: 1042, Query cover: 100%, E-Value: 0, Ident: 98%, Accession number: XM_019988567.1 [14]
    • Bos mutus DNA nucleotidylexotransferase (DNTT), transcript variant X1, mRNA, Max score: 1038, Query cover: 100%, E-Value: 0.0, Ident: 98%, Accession number: XM_005898843.1 [15]
  • Equivalent E. coli / JCVI functional protein: None found

Expression

  • Expression Level: high (chosen because no data on expression level was found for this gene)
  • Expression Level Hypothesis: This is not an E. coli gene, so an expression level could not be found for it in the E. coli protein count database. A high expression level was set by default.
  • Expression Level References and Description: [16]
  • Expression Time: Late
  • Expression Time Hypothesis: TdT is mainly used to repair cut or broken DNA or for random sequence production in a multicellular organism's immune system. It is not needed for regular function in bacteria, and can be expressed later than most other proteins since not many other genes will depend on it.
  • Expression Time References and Description: [17]

Gene Context

  • Other Components: None. This gene codes for a protein without any other subunits
  • Possible Dependencies: DNA polymerase III, alpha subunit DNA must be produced by other polymerases for TdT to add bases onto and repair.
  • Process: template-independent DNA elongation
    • Inputs: DNA(n), dNTP
    • Outputs: DNA(n + 1), PPi
    • Reference: [18]

Construct

  • Predicted Translation Rate:
  • Design Notes:
  • GenBank File: A link to the GenBank file. file