EG11013

From BioE80 Boot
Jump to: navigation, search

Author Information

Sruthi Raguveer

Basic Information

  • ID: EG11013
  • Name: topA
  • Organism: E. coli
  • Description: This gene codes for DNA topoisomerase 1. Topoisomerases are an essential group of proteins that deal with DNA topology. DNA topoisomerase 1 relaxes supercoiled DNA and hence relieves torsional tension that is created during replication and translation UniProt. The topoisomerase achieves this through creating a single strand break in the duplex DNA through transesterification that allows one strand to remove its supercoils. The DNA is then religated and the phosphodiester backbone is restored.
  • DNA Length: 2598 base pairs.
  • DNA sequence:

ATG GGT AAG GCC CTG GTC ATT GTA GAG TCT CCG GCA AAA GCT AAA ACC ATT AAT AAG TAC TTG GGC TCA GAC TAT GTA GTC AAA TCG TCG GTA GGT CATATC CGC GAT TTA CCT ACC TCC GGT TCG GCA GCG AAG AAG TCA GCG GAC TCT ACA TCT ACT AAG ACG GCA AAG AAG CCG AAA AAG GAT GAG CGT GGG GCATTG GTT AAT CGC ATG GGA GTT GAC CCT TGG CAT AAC TGG GAG GCA CAC TAT GAG GTG CTG CCC GGT AAG GAG AAA GTT GTG AGC GAG CTT AAA CAG CTGGCG GAA AAA GCA GAT CAT ATT TAT CTT GCG ACA GAT TTG GAC CGT GAG GGT GAG GCG ATT GCT TGG CAT CTT CGT GAG GTG ATC GGT GGG GAT GAC GCGCGC TAT TCA CGT GTG GTG TTC AAC GAG ATT ACC AAG AAT GCT ATC CGC CAG GCA TTC AAC AAG CCG GGC GAG CTG AAT ATT GAC CGT GTA AAT GCT CAACAA GCG CGT CGC TTT ATG GAC CGT GTT GTG GGA TAT ATG GTG TCG CCA TTA CTG TGG AAG AAG ATT GCC CGT GGG TTA TCG GCA GGG CGC GTA CAG TCAGTC GCA GTC CGC CTG GTG GTT GAA CGT GAA CGT GAA ATC AAA GCC TTT GTG CCG GAG GAG TTT TGG GAA GTA GAC GCC TCT ACC ACC ACA CCC TCA GGAGAG GCC TTG GCA TTA CAG GTA ACA CAC CAA AAC GAT AAG CCG TTT CGT CCT GTC AAC AAG GAG CAG ACG CAG GCA GCC GTC TCA CTG CTT GAG AAG GCCCGT TAC TCT GTA TTG GAG CGT GAG GAC AAG CCT ACG ACG AGC AAA CCA GGT GCA CCT TTC ATT ACA TCA ACA TTA CAA CAA GCA GCA TCT ACA CGC TTAGGC TTC GGC GTT AAG AAG ACA ATG ATG ATG GCA CAA CGT CTG TAT GAA GCA GGG TAT ATT ACA TAC ATG CGC ACA GAC TCT ACA AAC TTA TCC CAA GATGCG GTT AAC ATG GTT CGC GGG TAC ATT TCA GAT AAT TTT GGA AAG AAG TAT CTT CCC GAG TCT CCT AAC CAA TAC GCC TCG AAA GAA AAT TCT CAA GAGGCA CAC GAG GCT ATT CGC CCA AGC GAC GTC AAT GTA ATG GCT GAG TCC CTG AAA GAC ATG GAA GCC GAC GCC CAA AAA CTT TAT CAA TTG ATT TGG CGCCAG TTT GTA GCG TGT CAG ATG ACG CCA GCG AAG TAC GAC TCG ACT ACG CTG ACA GTA GGC GCT GGA GAT TTT CGC CTG AAG GCC CGT GGT CGC ATT CTTCGT TTT GAT GGC TGG ACG AAG GTG ATG CCA GCC CTT CGT AAA GGC GAT GAG GAT CGT ATC TTG CCT GCT GTG AAT AAG GGA GAT GCT TTG ACC TTG GTCGAG CTG ACC CCG GCG CAG CAT TTC ACA AAA CCC CCC GCC CGT TTT AGT GAA GCT AGC TTG GTC AAA GAA TTA GAA AAG CGC GGG ATT GGC CGC CCT TCTACC TAT GCT AGC ATT ATT AGC ACG ATC CAA GAT CGT GGC TAT GTG CGT GTA GAG AAT CGC CGC TTC TAT GCA GAG AAG ATG GGC GAA ATC GTC ACA GATCGC CTG GAA GAA AAT TTT CGC GAG TTA ATG AAT TAT GAC TTT ACG GCG CAG ATG GAG AAC TCA TTG GAT CAA GTT GCC AAC CAC GAA GCT GAA TGG AAAGCC GTA CTG GAC CAC TTT TTC AGT GAT TTC ACT CAA CAA CTG GAC AAA GCT GAA AAG GAT CCC GAA GAG GGG GGA ATG CGC CCC AAT CAA ATG GTG TTGACA TCG ATT GAT TGT CCC ACG TGT GGA CGC AAG ATG GGC ATC CGC ACA GCC TCG ACT GGC GTA TTT CTG GGT TGC AGC GGA TAC GCA CTG CCT CCG AAGGAG CGT TGT AAA ACC ACC ATT AAC CTG GTT CCG GAG AAC GAA GTG CTG AAC GTG TTA GAG GGG GAG GAC GCT GAG ACC AAT GCG TTG CGC GCA AAG CGTCGT TGC CCG AAA TGT GGC ACC GCC ATG GAC AGC TAT TTG ATC GAC CCA AAG CGT AAG CTG CAT GTC TGC GGC AAC AAC CCG ACT TGC GAC GGC TAC GAAATT GAA GAA GGG GAG TTT CGC ATT AAG GGT TAT GAT GGA CCT ATT GTA GAA TGT GAA AAG TGT GGT TCG GAA ATG CAT CTG AAG ATG GGC CGT TTC GGTAAG TAT ATG GCC TGT ACC AAC GAG GAG TGT AAA AAT ACT CGC AAA ATT CTT CGT AAC GGA GAA GTA GCT CCG CCG AAG GAG GAT CCG GTA CCT TTA CCCGAA CTT CCC TGT GAA AAG AGT GAT GCT TAC TTC GTA TTA CGC GAC GGC GCT GCA GGT GTC TTC TTA GCG GCA AAT ACG TTT CCA AAA TCT CGT GAA ACACGT GCA CCT CTG GTC GAA GAA TTG TAT CGC TTC CGC GAT CGT TTA CCA GAA AAA CTG CGT TAC CTT GCT GAC GCC CCC CAG CAA GAC CCG GAA GGC AACAAA ACG ATG GTT CGC TTT TCG CGC AAG ACT AAG CAG CAG TAC GTT TCT AGC GAG AAG GAC GGA AAA GCG ACA GGA TGG AGT GCC TTC TAC GTG GAT GGGAAA TGG GTT GAG GGC AAA AAG TAA

  • Amino Acid length: 865 amino acids.
  • Amino Acid sequence:

MGKALVIVES PAKAKTINKY LGSDYVVKSS VGHIRDLPTS GSAAKKSADS TSTKTAKKPK KDERGALVNR MGVDPWHNWE AHYEVLPGKE KVVSELKQLA EKADHIYLAT DLDREGEAIA WHLREVIGGD DARYSRVVFN EITKNAIRQA FNKPGELNID RVNAQQARRF MDRVVGYMVS PLLWKKIARG LSAGRVQSVA VRLVVERERE IKAFVPEEFW EVDASTTTPS GEALALQVTH QNDKPFRPVN KEQTQAAVSL LEKARYSVLE REDKPTTSKP GAPFITSTLQ QAASTRLGFG VKKTMMMAQR LYEAGYITYM RTDSTNLSQD AVNMVRGYIS DNFGKKYLPE SPNQYASKEN SQEAHEAIRP SDVNVMAESL KDMEADAQKL YQLIWRQFVA CQMTPAKYDS TTLTVGAGDF RLKARGRILR FDGWTKVMPA LRKGDEDRIL PAVNKGDALT LVELTPAQHF TKPPARFSEA SLVKELEKRG IGRPSTYASI ISTIQDRGYV RVENRRFYAE KMGEIVTDRL EENFRELMNY DFTAQMENSL DQVANHEAEW KAVLDHFFSD FTQQLDKAEK DPEEGGMRPN QMVLTSIDCP TCGRKMGIRT ASTGVFLGCS GYALPPKERC KTTINLVPEN EVLNVLEGED AETNALRAKR RCPKCGTAMD SYLIDPKRKL HVCGNNPTCD GYEIEEGEFR IKGYDGPIVE CEKCGSEMHL KMGRFGKYMA CTNEECKNTR KILRNGEVAP PKEDPVPLPE LPCEKSDAYF VLRDGAAGVF LAANTFPKSR ETRAPLVEEL YRFRDRLPEK LRYLADAPQQ DPEGNKTMVR FSRKTKQQYV SSEKDGKATG WSAFYVDGKW VEGKK

Function and Homologs

  • Product: DNA topoisomerase 1
  • Closest homologous proteins:
    • DNA topoisomerase type I, omega protein (Shigella boydii Sb227), 1805/100%/100%, ABB66391.1
    • DNA topoisomerase I (Shigella boydii), 1803/100%/0/99%, WP_078166360.1
    • DNA topoisomerase I (Shigella flexneri CDC 796-83), 1803/99%/0/100%, EFW62199.1

Expression

  • Expression Level: medium
  • Expression Level Hypothesis: The gene expression for topA is likely at a medium level because it removes supercoiling due to replication and translation which is necessary to maintain DNA integrity. Translation is constantly occurring within a cell.
  • Expression Level References and Description: UniProt
  • Expression Time: early
  • Expression Time Hypothesis: This gene should be expressed early because translation will occur at the beginning stages of the organism's life in order to produce integral proteins and this protein must exist for the DNA post-translation to have the proper topology.
  • Expression Time References and Description: EcoCyc UniProt ID: UniProt

Gene Context

  • Other Components: There is only one protein in this functional module. No other components are necessary.
  • Possible Dependencies: RNA Polymerase DNA Topoisomerase 1 is mainly functional after translation and replication and so is likely dependent on polymerases.
  • Process: The main process is the relaxation of supercoiled DNA
    • Inputs: Supercoiled DNA, Mg2+
    • Outputs: Normal DNA
    • References: EcoCyc

Construct

We will handle this - not part of your assignment

  • Synthesis Score: The synthesis score: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details:
  • GenBank File: A link to the GenBank file. file