Difference between revisions of "Part:BBa K4034003"

 
 
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<partinfo>BBa_K4034003 short</partinfo>
 
<partinfo>BBa_K4034003 short</partinfo>
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<partinfo>BBa_K4034003 SequenceAndFeatures</partinfo>
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<br><br>
  
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<!-- Add more about the biology of this part here
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This part encodes the RNR protein, betasubunit. It is codon optimised for <i>E. coli</i> BL21.
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===Usage and Biology===
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<br/>
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<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K4034003 SequenceAndFeatures</partinfo>
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=Description=
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<br>
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RNR catalyzes the conversion of all four ribonucleotides triphosphates (NTPs) into the corresponding dNTPs, therefore providing the building blocks for the synthesis and repair of DNA. This conversion is achieved by the reduction of the C2’-OH bond. This biochemical pathway is the only de novo dNTP production method. The reduction occurs for all nucleotides at a single active site.
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RNR is divided into three classes I, which is further divided into class Ia, Ib, and Ic, II, and III.
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<br>
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==Protein Structure==
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<br>
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Class I RNR is composed of two homoderic subunits α and β. When active, both in eucaryotes and procaryotes, the two proteins are associated in a dimeric or other oligomeric form, such as (alpha)n(beta)m.
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Based on the subclass of RNR, the metal centre required for the radical production, differs. Despite the differences apparent in the classes of RNR, all three contain a conserved cysteine residue at the active site. This cysteine residue is possibly converted into a thiyl radical, initiating the substrate turnover, by abstraction of a hydrogen atom from a ribose ring of the substrate.
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The substrate binding active  site is located in the alpha 2 homodimer, encoded by nrdA. The binding site for the two irons is contained in the beta 2 homodimer, encoded by nrdB.
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<br>
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==Ia RNR==
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<br>
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RNR Ia is dependent from oxygen, contains a di-iron center (FeIII-O-FeIII), has two allosteric centers, can be inhibited by ATP, is distributed in Eukaryotes, eubacteria,
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archaea, bacteriophages, and virus, is either in the (alpha)2(beta)2 or (alpha)6(beta)6 form, and is encoded by the nrdA and nrdB genes.
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<br>
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=nrdB=
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The beta subunit contains the contains the metallocofactor (di-iron), required for the reduction initiation.
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<br>
  
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=Source of this part=
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<br>
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NCBI code:AAC75295.1 <br>
  
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=References=
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===Functional Parameters===
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<br>
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<partinfo>BBa_K4034003 parameters</partinfo>
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1. Torrents, E. (2014). Ribonucleotide reductases: essential enzymes for bacterial life. Frontiers in Cellular and Infection Microbiology, 4. doi:10.3389/fcimb.2014.00052
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<br>
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2. Matthias Kolberg, Kari R Strand, Pål Graff, K Kristoffer Andersson, Structure, function, and mechanism of ribonucleotide reductases, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1699, Issues 1–2, 2004, Pages 1-34, ISSN 1570-9639, https://doi.org/10.1016/j.bbapap.2004.02.007.

Latest revision as of 15:47, 16 October 2021


nrdB encodes the beta subunit of RNR.


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 730
  • 1000
    COMPATIBLE WITH RFC[1000]



This part encodes the RNR protein, betasubunit. It is codon optimised for E. coli BL21.


Description


RNR catalyzes the conversion of all four ribonucleotides triphosphates (NTPs) into the corresponding dNTPs, therefore providing the building blocks for the synthesis and repair of DNA. This conversion is achieved by the reduction of the C2’-OH bond. This biochemical pathway is the only de novo dNTP production method. The reduction occurs for all nucleotides at a single active site. RNR is divided into three classes I, which is further divided into class Ia, Ib, and Ic, II, and III.


Protein Structure


Class I RNR is composed of two homoderic subunits α and β. When active, both in eucaryotes and procaryotes, the two proteins are associated in a dimeric or other oligomeric form, such as (alpha)n(beta)m. Based on the subclass of RNR, the metal centre required for the radical production, differs. Despite the differences apparent in the classes of RNR, all three contain a conserved cysteine residue at the active site. This cysteine residue is possibly converted into a thiyl radical, initiating the substrate turnover, by abstraction of a hydrogen atom from a ribose ring of the substrate. The substrate binding active site is located in the alpha 2 homodimer, encoded by nrdA. The binding site for the two irons is contained in the beta 2 homodimer, encoded by nrdB.



Ia RNR


RNR Ia is dependent from oxygen, contains a di-iron center (FeIII-O-FeIII), has two allosteric centers, can be inhibited by ATP, is distributed in Eukaryotes, eubacteria, archaea, bacteriophages, and virus, is either in the (alpha)2(beta)2 or (alpha)6(beta)6 form, and is encoded by the nrdA and nrdB genes.


nrdB


The beta subunit contains the contains the metallocofactor (di-iron), required for the reduction initiation.

Source of this part


NCBI code:AAC75295.1

References


1. Torrents, E. (2014). Ribonucleotide reductases: essential enzymes for bacterial life. Frontiers in Cellular and Infection Microbiology, 4. doi:10.3389/fcimb.2014.00052
2. Matthias Kolberg, Kari R Strand, Pål Graff, K Kristoffer Andersson, Structure, function, and mechanism of ribonucleotide reductases, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Volume 1699, Issues 1–2, 2004, Pages 1-34, ISSN 1570-9639, https://doi.org/10.1016/j.bbapap.2004.02.007.