EG10746

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Author Information

Danny Pantuso

Basic Information

  • ID: EG10746
  • Name: polA
  • Organism: E. coli
  • UniProt ID: [1]
  • Description: DNA polymerase 1 (Pol 1) is a key enzyme involved in the maintenance and replication of DNA. As like most DNA polymerase, it is a vital protein for copying DNA without mutation. Unlike most polymerases, it is unique in that it combines two types of polymerase activities. Pol 1 is responsible for both a 5’ to 3’ exonuclease activity and a 3’ to 5’ proofreading exonuclease activity.

DNA polymerase is especially important to our field in that it was the first known DNA polymerase known of any kind, and is ubiquitous in prokaryotes (Ecocyc.org, 2017). Discovered in 1956, this tiny gene represents a monumental leap in our understanding of bioengineering and has paved the way for countless other cells and mythizations to occur. As a result of their finding this gene, both lead scientists, Professor Arthur Kornberg and Severo Ochoa, earned a Nobel Prize. (Wikipedia, 2017) DNA Pol I is 1 of 5 known DNA polymerases found within E. coli. While they are all vital to the function of the cell, DNA Pol 1 is the most common and thought to be the most important for DNA repair. In an experiment aimed at determining the exact function of DNA Pol I, scientists found that colonies that lacked this gene could grow and reproduce normally. However, when exposed to harmful, mutagen inducing elements such as UV light, the cells became damage and were extremely prone to degradation. In addition, while DNA replication happens at roughly 1000 nucleotides a second, Pol I processes DNA at only ~20 nucleotides a second, and falls off after incorporating only ~50 nucleotides. Thus, scientists concluded that its primary role is repair. DNA Pol I’s is composed of four domains with two separate enzymatic activities. The last domain on the protein proofreads the product of Pol I and can repair any missed base pairs almost immediately after the mistake has been identified. The other three domains function as helper polypeptides to facilitate the DNA polymerase activity.

  • DNA Length: 2787 base pairs.
  • DNA sequence:

atgGTTCAGA TCCCCCAAAA TCCACTTATC CTTGTAGATG GTTCATCTTA TCTTTATCGC GCATATCACG CGTTTCCCCC GCTGACTAAC AGCGCAGGCG AGCCGACCGG TGCGATGTAT GGTGTCCTCA ACATGCTGCG CAGTCTGATC ATGCAATATA AACCGACGCA TGCAGCGGTG GTCTTTGACG CCAAGGGAAA AACCTTTCGT GATGAACTGT TTGAACATTA CAAATCACAT CGCCCGCCAA TGCCGGACGA TCTGCGTGCA CAAATCGAAC CCTTGCACGC GATGGTTAAA GCGATGGGAC TGCCGCTGCT GGCGGTTTCT GGCGTAGAAG CGGACGACGT TATCGGTACT CTGGCGCGCG AAGCCGAAAA AGCCGGGCGT CCGGTGCTGA TCAGCACTGG CGATAAAGAT ATGGCGCAGC TGGTGACGCC AAATATTACG CTTATCAATA CCATGACGAA TACCATCCTC GGACCGGAAG AGGTGGTGAA TAAGTACGGC GTGCCGCCAG AACTGATCAT CGATTTCCTG GCGCTGATGG GTGACTCCTC TGATAACATT CCTGGCGTAC CGGGCGTCGG TGAAAAAACC GCGCAGGCAT TGCTGCAAGG TCTTGGCGGA CTGGATACGC TGTATGCCGA GCCAGAAAAA ATTGCTGGGT TGAGCTTCCG TGGCGCGAAA ACAATGGCAG CGAAGCTCGA GCAAAACAAA GAAGTTGCTT ATCTCTCATA CCAGCTGGCG ACGATTAAAA CCGACGTTGA ACTGGAGCTG ACCTGTGAAC AACTGGAAGT GCAGCAACCG GCAGCGGAAG AGTTGTTGGG GCTGTTCAAA AAGTATGAGT TCAAACGCTG GACTGCTGAT GTCGAAGCGG GCAAATGGTT ACAGGCCAAA GGGGCAAAAC CAGCCGCGAA GCCACAGGAA ACCAGTGTTG CAGACGAAGC ACCAGAAGTG ACGGCAACGG TGATTTCTTA TGACAACTAC GTCACCATCC TTGATGAAGA AACACTGAAA GCGTGGATTG CGAAGCTGGA AAAAGCGCCG GTATTTGCAT TTGATACCGA AACCGACAGC CTTGATAACA TCTCTGCTAA CCTGGTCGGG CTTTCTTTTG CTATCGAGCC AGGCGTAGCG GCATATATTC CGGTTGCTCA TGATTATCTT GATGCGCCCG ATCAAATCTC TCGCGAGCGT GCACTCGAGT TGCTAAAACC GCTGCTGGAA GATGAAAAGG CGCTGAAGGT CGGGCAAAAC CTGAAATACG ATCGCGGTAT TCTGGCGAAC TACGGCATTG AACTGCGTGG GATTGCGTTT GATACCATGC TGGAGTCCTA CATTCTCAAT AGCGTTGCCG GGCGTCACGA TATGGACAGC CTCGCGGAAC GTTGGTTGAA GCACAAAACC ATCACTTTTG AAGAGATTGC TGGTAAAGGC AAAAATCAAC TGACCTTTAA CCAGATTGCC CTCGAAGAAG CCGGACGTTA CGCCGCCGAA GATGCAGATG TCACCTTGCA GTTGCATCTG AAAATGTGGC CGGATCTGCA AAAACACAAA GGGCCGTTGA ACGTCTTCGA GAATATCGAA ATGCCGCTGG TGCCGGTGCT TTCACGCATT GAACGTAACG GTGTGAAGAT CGATCCGAAA GTGCTGCACA ATCATTCTGA AGAGCTCACC CTTCGTCTGG CTGAGCTGGA AAAGAAAGCG CATGAAATTG CAGGTGAGGA ATTTAACCTT TCTTCCACCA AGCAGTTACA AACCATTCTC TTTGAAAAAC AGGGCATTAA ACCGCTGAAG AAAACGCCGG GTGGCGCGCC GTCAACGTCG GAAGAGGTAC TGGAAGAACT GGCGCTGGAC TATCCGTTGC CAAAAGTGAT TCTGGAGTAT CGTGGTCTGG CGAAGCTGAA ATCGACCTAC ACCGACAAGC TGCCGCTGAT GATCAACCCG AAAACCGGGC GTGTGCATAC CTCTTATCAC CAGGCAGTAA CTGCAACGGG ACGTTTATCG TCAACCGATC CTAACCTGCA AAACATTCCG GTGCGTAACG AAGAAGGTCG TCGTATCCGC CAGGCGTTTA TTGCGCCAGA GGATTATGTG ATTGTCTCAG CGGACTACTC GCAGATTGAA CTGCGCATTA TGGCGCATCT TTCGCGTGAC AAAGGCTTGC TGACCGCATT CGCGGAAGGA AAAGATATCC ACCGGGCAAC GGCGGCAGAA GTGTTTGGTT TGCCACTGGA AACCGTCACC AGCGAGCAAC GCCGTAGCGC GAAAGCGATC AACTTTGGTC TGATTTATGG CATGAGTGCT TTCGGTCTGG CGCGGCAATT GAACATTCCA CGTAAAGAAG CGCAGAAGTA CATGGACCTT TACTTCGAAC GCTACCCTGG CGTGCTGGAG TATATGGAAC GCACCCGTGC TCAGGCGAAA GAGCAGGGCT ACGTTGAAAC GCTGGACGGA CGCCGTCTGT ATCTGCCGGA TATCAAATCC AGCAATGGTG CTCGTCGTGC AGCGGCTGAA CGTGCAGCCA TTAACGCGCC AATGCAGGGA ACCGCCGCCG ACATTATCAA ACGGGCGATG ATTGCCGTTG ATGCGTGGTT ACAGGCTGAG CAACCGCGTG TACGTATGAT CATGCAGGTA CACGATGAAC TGGTATTTGA AGTTCATAAA GATGATGTTG ATGCCGTCGC GAAGCAGATT CATCAACTGA TGGAAAACTG TACCCGTCTG GATGTGCCGT TGCTGGTGGA AGTGGGGAGT GGCGAAAACT GGGATCAGGC GCACtaa

  • Amino Acid length: 928 amino acids.
  • Amino Acid sequence:

MVQIPQNPLI LVDGSSYLYR AYHAFPPLTN SAGEPTGAMY GVLNMLRSLI MQYKPTHAAV VFDAKGKTFR DELFEHYKSH RPPMPDDLRA QIEPLHAMVK AMGLPLLAVS GVEADDVIGT LAREAEKAGR PVLISTGDKD MAQLVTPNIT LINTMTNTIL GPEEVVNKYG VPPELIIDFL ALMGDSSDNI PGVPGVGEKT AQALLQGLGG LDTLYAEPEK IAGLSFRGAK TMAAKLEQNK EVAYLSYQLA TIKTDVELEL TCEQLEVQQP AAEELLGLFK KYEFKRWTAD VEAGKWLQAK GAKPAAKPQE TSVADEAPEV TATVISYDNY VTILDEETLK AWIAKLEKAP VFAFDTETDS LDNISANLVG LSFAIEPGVA AYIPVAHDYL DAPDQISRER ALELLKPLLE DEKALKVGQN LKYDRGILAN YGIELRGIAF DTMLESYILN SVAGRHDMDS LAERWLKHKT ITFEEIAGKG KNQLTFNQIA LEEAGRYAAE DADVTLQLHL KMWPDLQKHK GPLNVFENIE MPLVPVLSRI ERNGVKIDPK VLHNHSEELT LRLAELEKKA HEIAGEEFNL SSTKQLQTIL FEKQGIKPLK KTPGGAPSTS EEVLEELALD YPLPKVILEY RGLAKLKSTY TDKLPLMINP KTGRVHTSYH QAVTATGRLS STDPNLQNIP VRNEEGRRIR QAFIAPEDYV IVSADYSQIE LRIMAHLSRD KGLLTAFAEG KDIHRATAAE VFGLPLETVT SEQRRSAKAI NFGLIYGMSA FGLARQLNIP RKEAQKYMDL YFERYPGVLE YMERTRAQAK EQGYVETLDG RRLYLPDIKS SNGARRAAAE RAAINAPMQG TAADIIKRAM IAVDAWLQAE QPRVRMIMQV HDELVFEVHK DDVDAVAKQI HQLMENCTRL DVPLLVEVGS GENWDQAH

Function and Homologs

  • Functional Category: A link to the functional category into which this gene falls. For example, DNA repair.
  • Product: DNA Polymerase I
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • DNA polymerase I [Escherichia coli] 1902 100% 0.0 99% [WP_000250009.1]
    • MULTISPECIES: DNA polymerase I [Proteobacteria] 1902 100% 0.0 100% [WP_000250006.1]
    • DNA polymerase I [Escherichia coli] 1902 100% 0.0 99% [WP_085457888.1]

Expression

  • Expression Level: Medium.
  • Expression Level Hypothesis: DNA Polymerase I is mainly responsible for the maintenance of DNA, a vital part of cell functioning. Thus, DNA polymerase has a medium expression rate so that the DNA is maintained and cared for, but isn't highly expressed because DNA is a relatively stable molecule and will not break down often. Thus, it is not necessary to have high levels of DNA Polymerase 1.
  • Expression Level References and Description: Mgenitalium database
  • Expression Time: Late
  • Expression Level Hypothesis: The cell does not need to immediately correct for small errors in the DNA.Small scale DNA degradation is often the result of time and decay, so it follows that this protein should be expressed later on the the cell lifecycle.
  • Expression Time References and Description: Gene description.

Gene Context

  • Other Components: dnaN [[2]]
  • Possible Dependencies: DNA metabolism
  • Process: 3'-5' exonuclease activity
    • Inputs: Deoxynucleoside triphosphate + DNA(n)
    • Outputs: diphosphate + DNA(n+1)

Construct

  • Synthesis Score: The synthesis score of your construct: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details: For example, had to use a rare codon to fix folding energy;
  • GenBank File: A link to the GenBank file. file