MMSYN1 0771

From BioE80 Boot
Jump to: navigation, search

Author Information

Pretom Shome (pshome@stanford.edu)

Basic Information

  • ID: MMSYN1_0771
  • Name: NrdE_NrdA: ribonucleoside-diphosphate reductase, alpha subunit
  • Organism: The source organism of the gene is JCVI-Syn3.0.
  • Description: This gene codes for the alpha subunit of ribonucleotide reductase, an enzyme that catalyzes the conversion of ribonucleotides into deoxyribonucleotides(1). As a result, it plays an important role in DNA synthesis. The rate of expression of this gene has downstream effects in the rate of reproduction of the cell itself. By controlling the amount of DNA synthesized over a certain time period, this gene ensures a constant ratio of cell mass to DNA(2) and thus allows for the cell to be fully prepared by the time it undergoes mitosis. This gene is helpful to the function of the cell because many cells cannot create DNA alone; they must synthesize DNA from RNA through this pathway.
  • DNA Length: 2163 base pairs.
  • DNA sequence:

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

  • Amino Acid length: 720 amino acids.
  • Amino Acid sequence:

MKENKNTIVLDDVDDEYIKLNARSKIFSKDQDNFQLDVKAAELYLKNYIEPRMKKFSSLKERLDYLLENKYYDSEILNKYSFDQISQLNDYAYSFNHHFPSFMGALKFFNAYGLKTFDTTMYLETYTDRVLMNALFLGNGNFTKAKNLLKDMMLGRFQPATPTFLNAAKKHRGEYVSCYLLRTEDNMESICRTISTSLQLSKRGGGVAICLTNLRETGSPIKNISGLSSGPIPVMKILEDSFTYADQLGQRQGAGAVYISAHHPDIISVLDTKRENADEKIRIKSLSLGLVIPDITFELARDNKDMALFSPYDVQKVYNKPLSDISITEKYYEMLENPNIKKTYISARKFFLTVAELHFESGYPYILFEDTVNRRNAHDKKGRIIMSNLCSEIVQVSTASEYSSDLSFVKTGEDICCNLGSLNIDKMMKSGKEFSDSIYNAISALDIVSRNSDLSAAPSIQKGNAQNHAVGLGAMNLHGFLATNKIMYDSPEAVDFTNMFFYTVAYNAFKASNKLAQEFEKFASFDESRFADGSWFDKYTKCEFDKWTPQTNRVKELFKDYDVQIPSQTDWIQLVEEIKKTGLANSHLMAVAPTGSISYLSSCTPSLQPVVSTVEVRKEGKLGRVYVPAYQINFDNMGYYAMGAYELGADPIINIVAAAQQHVDQAISLTLFMTDKATTRDLNRAYVNAFKQGCSSIYYVRIRQDVLENSENYECDACKI

Function and Homologs

  • Product: ribonucleoside-diphosphate reductase, alpha subunit
  • Module: ribonucleoside-diphosphate reductase
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • ribonucleotide-diphosphate reductase subunit alpha [Escherichia coli] 766 766 97% 0.0 53% WP_077519455.1
    • ribonucleotide-diphosphate reductase [Escherichia coli] 766 766 97% 0.0 53% WP_024230428.1
    • ribonucleotide-diphosphate reductase subunit alpha [Escherichia coli] 766 766 97% 0.0 53% WP_074325926.1

Expression

  • Expression Level: low
  • Expression Level Hypothesis: As this enzyme catalyzes conversion of RNA to DNA, it has a broader role in the regulation of the frequency of reproduction. Its low level of expression means it likely acts as a rate-limiting enzyme that controls the rate of reproduction for the cell as a whole.
  • Expression Level References and Description: File:MgenitaliumSimProteinCounts.xlsx
  • Expression Time: Late
  • Expression Level Hypothesis: Since this gene is more involved in reproduction and is not as important in establishing a functional cell as components of the central dogma, this enzyme can be expressed later.
  • Expression Time References and Description: I made this decision by considering the roles that this enzyme has in a cell. Although the gene is very important to function, since it is mostly involved in regulation of reproduction rates, it is not necessary to express it at the beginning.

Gene Context

  • Other Components: Beta Subunit
  • Possible Dependencies: This gene is dependent on the beta subunit of the reductase enzyme. The alpha subunit cannot function without its counterpart. In the context of broader cellular function, this gene is dependent on translation as well, as RNA must first be formed before this step can be implemented.
  • Process: This enzyme is involved in the process to convert RNA to DNA. This pathway is iron-dependent(3) and creates the DNA used in DNA synthesis.
    • Inputs: RNA, Iron, ATP/GTP
    • Outputs: DNA, ADP, GDP

References

  • 1: Elledge SJ, Zhou Z, Allen JB (March 1992). "Ribonucleotide reductase: regulation, regulation, regulation". Trends Biochem. Sci. 17 (3): 119–23. doi:10.1016/0968-0004(92)90249-9. PMID 1412696.
  • 2: Herrick J, Sclavi B (January 2007). "Ribonucleotide reductase and the regulation of DNA replication: an old story and an ancient heritage". Mol. Microbiol. 63 (1): 22–34. doi:10.1111/j.1365-2958.2006.05493.x. PMID 17229208.
  • 3: Jordan A, Reichard P (1998). "Ribonucleotide reductases". Annu. Rev. Biochem. 67 (1): 71–98. doi:10.1146/annurev.biochem.67.1.71. PMID 9759483.