Team:NYMU-Taipei/ymim2

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Enzyme
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<title>NYMU iGEM</title>
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Substrate
 
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Kcat (min-1)
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    <script type="text/javascript">
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    <!--
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    $(function () {
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        $('ul.drawers').accordion({
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            header: 'H2.drawer-handle',
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Km(mM)
 
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<body>
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Organism
 
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<div class="ymi_spacer"></div>
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<div id="ymi_topcontainer">
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Reference
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    <div id="ymi_top">
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    <a
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href="http://2012.igem.org/Team:NYMU-Taipei/ymiproject.html" target="_parent">Project Venusian</a> ·
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    <a
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href="http://2012.igem.org/Team:NYMU-Taipei/ymim1" target="_parent">Modeling</a> ·
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    <a
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href="http://2012.igem.org/Team:NYMU-Taipei/ymihpa.html">Human Practice</a> ·
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    <a
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href="http://2012.igem.org/Team:NYMU-Taipei/ymijf.html">Extras</a> ·
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    <a
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href="http://2012.igem.org/Team:NYMU-Taipei/ymit1">Team</a> ·
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    <a href="http://2012.igem.org/Main_Page">iGEM</a>
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    </div>
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</div>
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  <div id="ymi_container_header">
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Nitrate Reductase (Nap)
 
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  <div id="ymi_header">
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      <div id="inner_header">
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      <a href="http://2012.igem.org/Team:NYMU-Taipei"><img src="http://2012.igem.org/wiki/images/7/7d/Ymi_header.jpg" border="0"></a>
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<div class="ymi_spacer_header"></div>
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  <div id="ymi_container">
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      <div id="ymi_left_column">
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<div class="text_area" align="justify">
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<div class="title">Modeling</div>
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<div align="left">
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  <p><span class="subtitle">Results </span></p>
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</div>
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<div align="left">
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  <p><img src="images/m2.gif" alt="" width="630" height="397" /><br />
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    In the figure  above, it showed that most nitrates were converted into ammonia. And the  productivity of nitrogen was quite low.</p>
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  <p><img src="images/m3.gif" alt="" width="630" height="324" />After 1440 min(1  day), only 10-12 mM of nitrogen were produced by an E.coli. But if  we combined the cell growth of E.coli with the equation, the result would be  different.</p>
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  <p><img src="images/m4.gif" alt="" width="630" height="324" />This figure  showed us the relationship between different enzyme concentration and time.<br />
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  </p>
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</div>
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<div align="left">
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  <div align="left">
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    <p><span class="subtitle">Conclusion</span></p>
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  </div>
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</div>
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<div align="left">
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  <p>Even though the  concentration of nitrogen we produced was low, but the toxicity of ammonia was  much lower than the NOx produced by the industrial factories. It might still be  a good way to apply our pathway to eliminate the toxic NOx compounds.</p>
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    <br />
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  </p>
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</div>
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<div align="left">
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  <div align="left">
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    <p><span class="subtitle">Parameters</span></p>
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      </div>
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  </div>
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<div align="left">
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  <table border="1" cellspacing="0" cellpadding="0">
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    <tr>
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      <td width="234" valign="top"><p>Enzyme</p></td>
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      <td width="142" valign="top"><p>Substrate</p></td>
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      <td width="113" valign="top"><p>Kcat (min-1)</p></td>
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      <td width="134" valign="top"><p>Km(mM)</p></td>
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      <td width="216" valign="top"><p>Organism</p></td>
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      <td width="104" valign="top"><p>Reference</p></td>
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        </tr>
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    <tr>
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      <td width="234" valign="top"><p>Nitrate Reductase (Nap)</p></td>
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      <td width="142" valign="top"><p>Nitrate</p></td>
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      <td width="113" valign="top"><p>3480</p></td>
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      <td width="134" valign="top"><p>0.112</p></td>
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      <td width="216" valign="top"><p><em>Paracoccus    pantotrophus</em></p></td>
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      <td width="104" valign="top"><p>(1)</p></td>
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        </tr>
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    <tr>
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      <td width="234" valign="top"><p>Nitrite Reductase (Nir)</p></td>
 +
      <td width="142" valign="top"><p>Nitrite</p></td>
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      <td width="113" valign="top"><p>480</p></td>
 +
      <td width="134" valign="top"><p>0.053</p></td>
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      <td width="216" valign="top"><p><em>Pseudomonas    aeruginosa</em></p></td>
 +
      <td width="104" valign="top"><p>(2)</p></td>
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        </tr>
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    <tr>
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      <td width="234" valign="top"><p>Nitric Oxide Reductase (Nor)</p></td>
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      <td width="142" valign="top"><p>Nitric Oxide</p></td>
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      <td width="113" valign="top"><p>12660</p></td>
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      <td width="134" valign="top"><p>0.06</p></td>
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      <td width="216" valign="top"><p><em>Fusarium    oxysporum</em></p></td>
 +
      <td width="104" valign="top"><p>(3)</p></td>
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        </tr>
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    <tr>
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      <td width="234" valign="top"><p>Nitrous Oxide Reductase (Nos)</p></td>
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      <td width="142" valign="top"><p>Nitrous Oxide</p></td>
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      <td width="113" valign="top"><p>16800</p></td>
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      <td width="134" valign="top"><p>0.0056</p></td>
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      <td width="216" valign="top"><p><em>Paracoccus    denitrificans</em></p></td>
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      <td width="104" valign="top"><p>(4)</p></td>
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        </tr>
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      </table>
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  <br />
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  <br />
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          <table border="1" cellspacing="0" cellpadding="0">
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            <tr>
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              <td width="215" valign="top"><p>Enzyme</p></td>
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              <td width="123" valign="top"><p>Substrate</p></td>
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              <td width="151" valign="top"><p>Vmax (mM /min-1)</p></td>
 +
              <td width="134" valign="top"><p>Km(mM)</p></td>
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              <td width="216" valign="top"><p>Organism</p></td>
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              <td width="104" valign="top"><p>Reference</p></td>
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            </tr>
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            <tr>
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              <td width="215" valign="top"><p>Nitrate Reductase (Nap)</p></td>
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              <td width="123" valign="top"><p>Nitrate</p></td>
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              <td width="151" valign="top"><p>27.885</p></td>
 +
              <td width="134" valign="top"><p>0.47</p></td>
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              <td width="216" valign="top"><p><em>Escherichia    coli</em></p></td>
 +
              <td width="104" valign="top"><p>(5)</p></td>
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            </tr>
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            <tr>
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              <td width="215" valign="top"><p>Nitrite Reductase (Nfr)</p></td>
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              <td width="123" valign="top"><p>Nitrite</p></td>
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              <td width="151" valign="top"><p>46.14</p></td>
 +
              <td width="134" valign="top"><p>0.022</p></td>
 +
              <td width="216" valign="top"><p><em>Escherichia    coli</em></p></td>
 +
              <td width="104" valign="top"><p>(6)</p></td>
 +
            </tr>
 +
            <tr>
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              <td width="215" valign="top"><p>Nitrite Reductase (Nir)</p></td>
 +
              <td width="123" valign="top"><p>Nitrite</p></td>
 +
              <td width="151" valign="top"><p>0.465</p></td>
 +
              <td width="134" valign="top"><p>0.4</p></td>
 +
              <td width="216" valign="top"><p><em>Escherichia    coli</em></p></td>
 +
              <td width="104" valign="top"><p>(7)</p></td>
 +
            </tr>
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          </table>
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          <br />
 +
          <br />
 +
          <table border="1" cellspacing="0" cellpadding="0">
 +
            <tr>
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              <td width="147" valign="top"><p>Parameter</p></td>
 +
              <td width="162" valign="top"><p>Description</p></td>
 +
              <td width="95" valign="top"><p>Value</p></td>
 +
              <td width="132" valign="top"><p>Units</p></td>
 +
              <td width="158" valign="top"><p>Reference</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image002.png" alt="" width="56" height="21" /></p></td>
 +
              <td width="162" valign="top"><p>Copy Number in E.coli</p></td>
 +
              <td width="95" valign="top"><p>300</p></td>
 +
              <td width="132" valign="top"><p>Copy Number per Cell</p></td>
 +
              <td width="158" valign="top"><p>Part Registry</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image004.png" alt="" width="10" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Ptrc Promoter Strength</p></td>
 +
              <td width="95" valign="top"><p>0.00003156</p></td>
 +
              <td width="132" valign="top"><p>Polymerase per min</p></td>
 +
              <td width="158" valign="top"><p>(10)(11)(12)</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image006.png" alt="" width="43" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Degradation Rate of mRNA in E.coli</p></td>
 +
              <td width="95" valign="top"><p>0.102</p></td>
 +
              <td width="132" valign="top"><p>min-1</p></td>
 +
              <td width="158" valign="top"><p>(8)</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image008.png" alt="" width="53" height="21" /></p></td>
 +
              <td width="162" valign="top"><p>Degradation Rate of Enzyme in E.coli</p></td>
 +
              <td width="95" valign="top"><p>0.0348</p></td>
 +
              <td width="132" valign="top"><p>min-1</p></td>
 +
              <td width="158" valign="top"><p>(8)</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image010.png" alt="" width="10" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Translation rate in E.coli</p></td>
 +
              <td width="95" valign="top"><p>720~1260</p></td>
 +
              <td width="132" valign="top"><p>Amino Acids/min</p></td>
 +
              <td width="158" valign="top"><p>(9)</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image012.png" alt="" width="18" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Avogadaros' Number </p></td>
 +
              <td width="95" valign="top"><p>6.02*<img src="m2_clip_image014.png" alt="" width="31" height="19" /></p></td>
 +
              <td width="132" valign="top"><p>mmole-1</p></td>
 +
              <td width="158" valign="top"><p>N/A</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image016.png" alt="" width="39" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Cell Volume of E.coli</p></td>
 +
              <td width="95" valign="top"><p>6.5*<img src="m2_clip_image018.png" alt="" width="40" height="19" /></p></td>
 +
              <td width="132" valign="top"><p>liter </p></td>
 +
              <td width="158" valign="top"><p>(18)</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image020.png" alt="" width="36" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Translation rate of Nap</p></td>
 +
              <td width="95" valign="top"><p>0.763</p></td>
 +
              <td width="132" valign="top"><p>Number of mRNA/min</p></td>
 +
              <td width="158" valign="top"><p>Estimated</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image022.png" alt="" width="36" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Translation rate of Nir</p></td>
 +
              <td width="95" valign="top"><p>0.96</p></td>
 +
              <td width="132" valign="top"><p>Number of mRNA/min</p></td>
 +
              <td width="158" valign="top"><p>Estimated</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image024.png" alt="" width="36" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Translation rate of Nor</p></td>
 +
              <td width="95" valign="top"><p>1.668</p></td>
 +
              <td width="132" valign="top"><p>Number of mRNA/min</p></td>
 +
              <td width="158" valign="top"><p>Estimated</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image026.png" alt="" width="36" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Translation rate of Nos</p></td>
 +
              <td width="95" valign="top"><p>1.602</p></td>
 +
              <td width="132" valign="top"><p>Number of mRNA/min</p></td>
 +
              <td width="158" valign="top"><p>Estimated</p></td>
 +
            </tr>
 +
          </table>
 +
          <table border="1" cellspacing="0" cellpadding="0">
 +
            <tr>
 +
              <td width="147" valign="top"><p>Parameter</p></td>
 +
              <td width="162" valign="top"><p>Description</p></td>
 +
              <td width="95" valign="top"><p>Value</p></td>
 +
              <td width="132" valign="top"><p>Units</p></td>
 +
              <td width="158" valign="top"><p>Reference</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image002_0000.png" alt="" width="56" height="21" /></p></td>
 +
              <td width="162" valign="top"><p>Copy Number in E.coli</p></td>
 +
              <td width="95" valign="top"><p>300</p></td>
 +
              <td width="132" valign="top"><p>Copy Number per Cell</p></td>
 +
              <td width="158" valign="top"><p>Part Registry</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image004_0000.png" alt="" width="10" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Ptrc Promoter Strength</p></td>
 +
              <td width="95" valign="top"><p>0.00003156</p></td>
 +
              <td width="132" valign="top"><p>Polymerase per min</p></td>
 +
              <td width="158" valign="top"><p>(8)(9)(10)</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image006_0000.png" alt="" width="43" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Degradation Rate of mRNA in E.coli</p></td>
 +
              <td width="95" valign="top"><p>0.102</p></td>
 +
              <td width="132" valign="top"><p>min-1</p></td>
 +
              <td width="158" valign="top"><p>(11)</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image008_0000.png" alt="" width="53" height="21" /></p></td>
 +
              <td width="162" valign="top"><p>Degradation Rate of Enzyme in E.coli</p></td>
 +
              <td width="95" valign="top"><p>0.0348</p></td>
 +
              <td width="132" valign="top"><p>min-1</p></td>
 +
              <td width="158" valign="top"><p>(11)</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image010_0000.png" alt="" width="10" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Translation rate in E.coli</p></td>
 +
              <td width="95" valign="top"><p>720~1260</p></td>
 +
              <td width="132" valign="top"><p>Amino Acids/min</p></td>
 +
              <td width="158" valign="top"><p>(12)</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image012_0000.png" alt="" width="18" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Avogadaros' Number </p></td>
 +
              <td width="95" valign="top"><p>6.02*<img src="m2_clip_image014_0000.png" alt="" width="31" height="19" /></p></td>
 +
              <td width="132" valign="top"><p>mmole-1</p></td>
 +
              <td width="158" valign="top"><p>N/A</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image016_0000.png" alt="" width="39" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Cell Volume of E.coli</p></td>
 +
              <td width="95" valign="top"><p>6.5*<img src="m2_clip_image018_0000.png" alt="" width="40" height="19" /></p></td>
 +
              <td width="132" valign="top"><p>liter </p></td>
 +
              <td width="158" valign="top"><p>(13)</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image020_0000.png" alt="" width="36" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Translation rate of Nap</p></td>
 +
              <td width="95" valign="top"><p>0.763</p></td>
 +
              <td width="132" valign="top"><p>Number of mRNA/min</p></td>
 +
              <td width="158" valign="top"><p>Estimated</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image022_0000.png" alt="" width="36" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Translation rate of Nir</p></td>
 +
              <td width="95" valign="top"><p>0.96</p></td>
 +
              <td width="132" valign="top"><p>Number of mRNA/min</p></td>
 +
              <td width="158" valign="top"><p>Estimated</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image024_0000.png" alt="" width="36" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Translation rate of Nor</p></td>
 +
              <td width="95" valign="top"><p>1.668</p></td>
 +
              <td width="132" valign="top"><p>Number of mRNA/min</p></td>
 +
              <td width="158" valign="top"><p>Estimated</p></td>
 +
            </tr>
 +
            <tr>
 +
              <td width="147" valign="top"><p><img src="m2_clip_image026_0000.png" alt="" width="36" height="19" /></p></td>
 +
              <td width="162" valign="top"><p>Translation rate of Nos</p></td>
 +
              <td width="95" valign="top"><p>1.602</p></td>
 +
              <td width="132" valign="top"><p>Number of mRNA/min</p></td>
 +
              <td width="158" valign="top"><p>Estimated</p></td>
 +
            </tr>
 +
          </table>
 +
          <p><br />
 +
</p>
 +
<div align="left">
 +
  <div align="left">
 +
    <p><span class="subtitle">Reference</span></p>
 +
  </div>
 +
</div>
 +
  <p>[1]Andrew J. GATES, David J. RICHARDSON,  Julea N. BUTT(2008) Voltammetric characterization of the aerobic  energy-dissipating nitrate reductase of Paracoccus pantotrophus : exploring the  activity of a redox-balancing enzyme as a f unction of electrochemical  potential. Biochem. J. (2008) 409, 159–168</p>
 +
          <p>[2]Serena Rinaldo, Francesca Cutruzzolà(2007)  Nitrite Reductases in Denitrification. Biology of the Nitrogen Cycle 37-55</p>
 +
          <p>[3]Naoki Toritsuka, Hirofumi Shoun, Udai P.  Singh, Sam-Yong Park , Tetsutaro Iizuka, Yoshitsugu Shiro(1997) Functional and  structural comparison of nitric oxide reductases from denitrifying fungi  Cylindrocarpon tonkinense and Fusarium oxysporum. Biochimica et Biophysica Acta  1338 1997 93–99</p>
 +
          <p>[4]Stuart W. Snyder, Thomas C. Hollocher(1987)  Purification and some characteristics of   nitrous oxide reductase from Paracoccus denitrificans. The Journal of Biology  Chemistry VOl. 262, No.14. Issue of May 15. , pp. 6515-6525</p>
 +
          <p>[5] Robert A. LAZZARINI, Daniel E. Atkinson(1961)  A Triphosphopyridine Nucleotide-specific Nitrite Reductase from Escherichia coli.  The Journal of Biology Chemistry VOl. 236, No.12. December</p>
 +
          <p>[6] Michael W. W. AdamsS, Leonard E.  Mortenson(1982) The Effect of Cyanide and Ferricyanide on the Activity of the  Dissimilatory Nitrate Reductase of Escherichia coli. The Journal of Biology Chemistry  VOl. 257, No.4. Issue of February 25, pp. 1791-1799<br />
 +
            <br />
 +
            [7] Lewis M. Siegel, David C. Rueger,  Michael J. Barber, Rick J. Krueger(1982) Escherichia coli Sulfite Reductase Hemoprotein  Subuni. The Journal of Biology Chemistry VOl. 257, No.11. Issue of June 10, pp.  6343-6350</p>
 +
          <p>[8] Hsin-Ho Huang, Daniel Camsund, Peter  Lindblad and Thorsten Heidorn(2010) Design and characterization of molecular  tools for a Synthetic Biology approach towards developing cyanobacterial  biotechnology. Nucleic Acids Research, Vol. 38, No. 8 2577–2593</p>
 +
          <p>[9] Michael Brunner, Hermann Bujard(1987) Promoter  recognition and promoter strength in the Escherichia coli system. The EMBO Journal  vol.6 no.10 pp.3139-3144</p>
 +
          <p>[10]Thomas A . Clarke , Paul C. Mills,  Susie R. Poock,bJulea N. Butt, Myles R. Cheesman, Jeffrey A. Cole, Jay C. D.  Hinton, Andrew M. Hemmings, Gemma Kemp, Christopher A . G . So¨derberg, Stephen  Spiro, Jessica Van Wonderen, David J. Richardson(2008)Escherichia coli  Cytochrome c Nitrite Reductase NrfA. Methods in Enzymology, Vol. 437 pp.64-77</p>
 +
          <p>[11] Kmalendu Nath, Arthur L. Koch(1971) Protein  Degradation in Escherichia coli. The Journal of Biology Chemistry VOl. 246, No.22.  Issue of November 25, pp. 6956-6967</p>
 +
          <p>[12]Thomas A . Clarke , Paul C. Mills,  Susie R. Poock,bJulea N. Butt, Myles R. Cheesman, Jeffrey A. Cole, Jay C. D.  Hinton, Andrew M. Hemmings, Gemma Kemp, Christopher A . G . So¨derberg, Stephen  Spiro, Jessica Van Wonderen, David J. Richardson(2008)Escherichia coli  Cytochrome c Nitrite Reductase NrfA. Methods in Enzymology, Vol. 437 pp.64-77</p>
 +
          <p>[13] Cell Volume Increase in Escherichia  coli after Shifts to Richer Media, H. E. KUBITSCHEK ,Biological and Medical  Research Division, Argonne National Laboratory,9700 South Cass Avenue, Argonne,  Illinois 60439</p>
 +
          <p><br />
 +
          </p>
 +
  </div>
 +
</div>
 +
      </div>
 +
   
 +
    <div id="ymi_right_column">
 +
          <div class="drawers-wrapper">
 +
<div class="boxcap captop"></div>
 +
    <ul class="drawers">
 +
        <li class="drawer">
 +
       
 +
<h2 class="drawer-handle">Modeling</h2>
-
Nitrate
+
            <ul>
 +
                <li><a title="Description" href="http://2012.igem.org/Team:NYMU-Taipei/ymim1">Description</a></li>
 +
                <li><a title="Results & Conclusion" href="http://2012.igem.org/Team:NYMU-Taipei/ymim2">Results & Conclusion<br />
 +
                  <br />
 +
                </a></li>
 +
                                             
 +
          </ul> 
 +
       
 +
       
 +
       
 +
       
 +
       
 +
       
 +
       
-
3480
+
        </li>
 +
        <li class="drawer">        </li>
-
0.112
 
-
Paracoccus pantotrophus
+
        <li class="drawer last">
 +
         
 +
         
 +
         
 +
         
 +
         
 +
         
 +
         
 +
         
 +
         
 +
         
 +
         
 +
        </li>
 +
    </ul>
 +
<div class="boxcap"></div>
 +
</div>
 +
  </div>
 +
 +
<div id="ymi_footer">
 +
    </div>
 +
       
 +
</div>
-
(1)
 
-
Nitrite Reductase (Nir)
 
-
 
+
<div class="ymi_spacer"></div>
-
 
+
</div>
-
Nitrite
+
</body>
-
 
+
</html>
-
 
+
-
 
+
-
480
+
-
 
+
-
 
+
-
 
+
-
0.053
+
-
 
+
-
 
+
-
 
+
-
Pseudomonas aeruginosa
+
-
 
+
-
 
+
-
 
+
-
(2)
+
-
 
+
-
 
+
-
 
+
-
Nitric Oxide Reductase (Nor)
+
-
 
+
-
 
+
-
 
+
-
Nitric Oxide
+
-
 
+
-
 
+
-
 
+
-
12660
+
-
 
+
-
 
+
-
 
+
-
0.06
+
-
 
+
-
 
+
-
 
+
-
Fusarium oxysporum
+
-
 
+
-
 
+
-
 
+
-
(3)
+
-
 
+
-
 
+
-
 
+
-
Nitrous Oxide Reductase (Nos)
+
-
 
+
-
 
+
-
 
+
-
Nitrous Oxide
+
-
 
+
-
 
+
-
 
+
-
16800
+
-
 
+
-
 
+
-
 
+
-
0.0056
+
-
 
+
-
 
+
-
 
+
-
Paracoccus denitrificans
+
-
 
+
-
 
+
-
 
+
-
(4)
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Enzyme
+
-
 
+
-
 
+
-
 
+
-
Substrate
+
-
 
+
-
 
+
-
 
+
-
Vmax (mM /min-1)
+
-
 
+
-
 
+
-
 
+
-
Km(mM)
+
-
 
+
-
 
+
-
 
+
-
Organism
+
-
 
+
-
 
+
-
 
+
-
Reference
+
-
 
+
-
 
+
-
 
+
-
Nitrate Reductase (Nap)
+
-
 
+
-
 
+
-
 
+
-
Nitrate
+
-
 
+
-
 
+
-
 
+
-
27.885
+
-
 
+
-
 
+
-
 
+
-
0.47
+
-
 
+
-
 
+
-
 
+
-
Escherichia coli
+
-
 
+
-
 
+
-
 
+
-
(5)
+
-
 
+
-
 
+
-
 
+
-
Nitrite Reductase (Nfr)
+
-
 
+
-
 
+
-
 
+
-
Nitrite
+
-
 
+
-
 
+
-
 
+
-
46.14
+
-
 
+
-
 
+
-
 
+
-
0.022
+
-
 
+
-
 
+
-
 
+
-
Escherichia coli
+
-
 
+
-
 
+
-
 
+
-
(6)
+
-
 
+
-
 
+
-
 
+
-
Nitrite Reductase (Nir)
+
-
 
+
-
 
+
-
 
+
-
Nitrite
+
-
 
+
-
 
+
-
 
+
-
0.465
+
-
 
+
-
 
+
-
 
+
-
0.4
+
-
 
+
-
 
+
-
 
+
-
Escherichia coli
+
-
 
+
-
 
+
-
 
+
-
(7)
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Parameter
+
-
 
+
-
 
+
-
 
+
-
Description
+
-
 
+
-
 
+
-
 
+
-
Value
+
-
 
+
-
 
+
-
 
+
-
Units
+
-
 
+
-
 
+
-
 
+
-
Reference
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Copy Number in E.coli
+
-
 
+
-
 
+
-
 
+
-
300
+
-
 
+
-
 
+
-
 
+
-
Copy Number per Cell
+
-
 
+
-
 
+
-
 
+
-
Part Registry
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Ptrc Promoter Strength
+
-
 
+
-
 
+
-
 
+
-
0.00003156
+
-
 
+
-
 
+
-
 
+
-
Polymerase per min
+
-
 
+
-
 
+
-
 
+
-
(10)(11)(12)
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Degradation Rate of mRNA in E.coli
+
-
 
+
-
 
+
-
 
+
-
0.102
+
-
 
+
-
 
+
-
 
+
-
min-1
+
-
 
+
-
 
+
-
 
+
-
(8)
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Degradation Rate of Enzyme in E.coli
+
-
 
+
-
 
+
-
 
+
-
0.0348
+
-
 
+
-
 
+
-
 
+
-
min-1
+
-
 
+
-
 
+
-
 
+
-
(8)
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Translation rate in E.coli
+
-
 
+
-
 
+
-
 
+
-
720~1260
+
-
 
+
-
 
+
-
 
+
-
Amino Acids/min
+
-
 
+
-
 
+
-
 
+
-
(9)
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Avogadaros' Number
+
-
 
+
-
 
+
-
 
+
-
6.02*
+
-
 
+
-
 
+
-
 
+
-
mmole-1
+
-
 
+
-
 
+
-
 
+
-
N/A
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Cell Volume of E.coli
+
-
 
+
-
 
+
-
 
+
-
6.5*
+
-
 
+
-
 
+
-
 
+
-
liter
+
-
 
+
-
 
+
-
 
+
-
(18)
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Translation rate of Nap
+
-
 
+
-
 
+
-
 
+
-
0.763
+
-
 
+
-
 
+
-
 
+
-
Number of mRNA/min
+
-
 
+
-
 
+
-
 
+
-
Estimated
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Translation rate of Nir
+
-
 
+
-
 
+
-
 
+
-
0.96
+
-
 
+
-
 
+
-
 
+
-
Number of mRNA/min
+
-
 
+
-
 
+
-
 
+
-
Estimated
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Translation rate of Nor
+
-
 
+
-
 
+
-
 
+
-
1.668
+
-
 
+
-
 
+
-
 
+
-
Number of mRNA/min
+
-
 
+
-
 
+
-
 
+
-
Estimated
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Translation rate of Nos
+
-
 
+
-
 
+
-
 
+
-
1.602
+
-
 
+
-
 
+
-
 
+
-
Number of mRNA/min
+
-
 
+
-
 
+
-
 
+
-
Estimated
+
-
 
+
-
 
+
-
 
+
-
Parameter
+
-
 
+
-
 
+
-
 
+
-
Description
+
-
 
+
-
 
+
-
 
+
-
Value
+
-
 
+
-
 
+
-
 
+
-
Units
+
-
 
+
-
 
+
-
 
+
-
Reference
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Copy Number in E.coli
+
-
 
+
-
 
+
-
 
+
-
300
+
-
 
+
-
 
+
-
 
+
-
Copy Number per Cell
+
-
 
+
-
 
+
-
 
+
-
Part Registry
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Ptrc Promoter Strength
+
-
 
+
-
 
+
-
 
+
-
0.00003156
+
-
 
+
-
 
+
-
 
+
-
Polymerase per min
+
-
 
+
-
 
+
-
 
+
-
(8)(9)(10)
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Degradation Rate of mRNA in E.coli
+
-
 
+
-
 
+
-
 
+
-
0.102
+
-
 
+
-
 
+
-
 
+
-
min-1
+
-
 
+
-
 
+
-
 
+
-
(11)
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Degradation Rate of Enzyme in E.coli
+
-
 
+
-
 
+
-
 
+
-
0.0348
+
-
 
+
-
 
+
-
 
+
-
min-1
+
-
 
+
-
 
+
-
 
+
-
(11)
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Translation rate in E.coli
+
-
 
+
-
 
+
-
 
+
-
720~1260
+
-
 
+
-
 
+
-
 
+
-
Amino Acids/min
+
-
 
+
-
 
+
-
 
+
-
(12)
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Avogadaros' Number
+
-
 
+
-
 
+
-
 
+
-
6.02*
+
-
 
+
-
 
+
-
 
+
-
mmole-1
+
-
 
+
-
 
+
-
 
+
-
N/A
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Cell Volume of E.coli
+
-
 
+
-
 
+
-
 
+
-
6.5*
+
-
 
+
-
 
+
-
 
+
-
liter
+
-
 
+
-
 
+
-
 
+
-
(13)
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Translation rate of Nap
+
-
 
+
-
 
+
-
 
+
-
0.763
+
-
 
+
-
 
+
-
 
+
-
Number of mRNA/min
+
-
 
+
-
 
+
-
 
+
-
Estimated
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Translation rate of Nir
+
-
 
+
-
 
+
-
 
+
-
0.96
+
-
 
+
-
 
+
-
 
+
-
Number of mRNA/min
+
-
 
+
-
 
+
-
 
+
-
Estimated
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Translation rate of Nor
+
-
 
+
-
 
+
-
 
+
-
1.668
+
-
 
+
-
 
+
-
 
+
-
Number of mRNA/min
+
-
 
+
-
 
+
-
 
+
-
Estimated
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Translation rate of Nos
+
-
 
+
-
 
+
-
 
+
-
1.602
+
-
 
+
-
 
+
-
 
+
-
Number of mRNA/min
+
-
 
+
-
 
+
-
 
+
-
Estimated
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
Reference
+
-
 
+
-
 
+
-
 
+
-
 
+
-
 
+
-
[1]Andrew J. GATES, David J. RICHARDSON, Julea N. BUTT(2008) Voltammetric characterization of the aerobic energy-dissipating nitrate reductase of Paracoccus pantotrophus : exploring the activity of a redox-balancing enzyme as a f unction of electrochemical potential. Biochem. J. (2008) 409, 159–168
+
-
 
+
-
[2]Serena Rinaldo, Francesca Cutruzzolà(2007) Nitrite Reductases in Denitrification. Biology of the Nitrogen Cycle 37-55
+
-
 
+
-
[3]Naoki Toritsuka, Hirofumi Shoun, Udai P. Singh, Sam-Yong Park , Tetsutaro Iizuka, Yoshitsugu Shiro(1997) Functional and structural comparison of nitric oxide reductases from denitrifying fungi Cylindrocarpon tonkinense and Fusarium oxysporum. Biochimica et Biophysica Acta 1338 1997 93–99
+
-
 
+
-
[4]Stuart W. Snyder, Thomas C. Hollocher(1987) Purification and some characteristics of nitrous oxide reductase from Paracoccus denitrificans. The Journal of Biology Chemistry VOl. 262, No.14. Issue of May 15. , pp. 6515-6525
+
-
 
+
-
[5] Robert A. LAZZARINI, Daniel E. Atkinson(1961) A Triphosphopyridine Nucleotide-specific Nitrite Reductase from Escherichia coli. The Journal of Biology Chemistry VOl. 236, No.12. December
+
-
 
+
-
[6] Michael W. W. AdamsS, Leonard E. Mortenson(1982) The Effect of Cyanide and Ferricyanide on the Activity of the Dissimilatory Nitrate Reductase of Escherichia coli. The Journal of Biology Chemistry VOl. 257, No.4. Issue of February 25, pp. 1791-1799
+
-
 
+
-
[7] Lewis M. Siegel, David C. Rueger, Michael J. Barber, Rick J. Krueger(1982) Escherichia coli Sulfite Reductase Hemoprotein Subuni. The Journal of Biology Chemistry VOl. 257, No.11. Issue of June 10, pp. 6343-6350
+
-
 
+
-
[8] Hsin-Ho Huang, Daniel Camsund, Peter Lindblad and Thorsten Heidorn(2010) Design and characterization of molecular tools for a Synthetic Biology approach towards developing cyanobacterial biotechnology. Nucleic Acids Research, Vol. 38, No. 8 2577–2593
+
-
 
+
-
[9] Michael Brunner, Hermann Bujard(1987) Promoter recognition and promoter strength in the Escherichia coli system. The EMBO Journal vol.6 no.10 pp.3139-3144
+
-
 
+
-
[10]Thomas A . Clarke , Paul C. Mills, Susie R. Poock,bJulea N. Butt, Myles R. Cheesman, Jeffrey A. Cole, Jay C. D. Hinton, Andrew M. Hemmings, Gemma Kemp, Christopher A . G . So¨derberg, Stephen Spiro, Jessica Van Wonderen, David J. Richardson(2008)Escherichia coli Cytochrome c Nitrite Reductase NrfA. Methods in Enzymology, Vol. 437 pp.64-77
+
-
 
+
-
[11] Kmalendu Nath, Arthur L. Koch(1971) Protein Degradation in Escherichia coli. The Journal of Biology Chemistry VOl. 246, No.22. Issue of November 25, pp. 6956-6967
+
-
 
+
-
[12]Thomas A . Clarke , Paul C. Mills, Susie R. Poock,bJulea N. Butt, Myles R. Cheesman, Jeffrey A. Cole, Jay C. D. Hinton, Andrew M. Hemmings, Gemma Kemp, Christopher A . G . So¨derberg, Stephen Spiro, Jessica Van Wonderen, David J. Richardson(2008)Escherichia coli Cytochrome c Nitrite Reductase NrfA. Methods in Enzymology, Vol. 437 pp.64-77
+
-
 
+
-
[13] Cell Volume Increase in Escherichia coli after Shifts to Richer Media, H. E. KUBITSCHEK ,Biological and Medical Research Division, Argonne National Laboratory,9700 South Cass Avenue, Argonne, Illinois 60439
+

Revision as of 03:04, 27 September 2012

NYMU iGEM

Modeling

Results


In the figure above, it showed that most nitrates were converted into ammonia. And the productivity of nitrogen was quite low.

After 1440 min(1 day), only 10-12 mM of nitrogen were produced by an E.coli. But if we combined the cell growth of E.coli with the equation, the result would be different.

This figure showed us the relationship between different enzyme concentration and time.

Conclusion

Even though the concentration of nitrogen we produced was low, but the toxicity of ammonia was much lower than the NOx produced by the industrial factories. It might still be a good way to apply our pathway to eliminate the toxic NOx compounds.


Parameters

Enzyme

Substrate

Kcat (min-1)

Km(mM)

Organism

Reference

Nitrate Reductase (Nap)

Nitrate

3480

0.112

Paracoccus pantotrophus

(1)

Nitrite Reductase (Nir)

Nitrite

480

0.053

Pseudomonas aeruginosa

(2)

Nitric Oxide Reductase (Nor)

Nitric Oxide

12660

0.06

Fusarium oxysporum

(3)

Nitrous Oxide Reductase (Nos)

Nitrous Oxide

16800

0.0056

Paracoccus denitrificans

(4)



Enzyme

Substrate

Vmax (mM /min-1)

Km(mM)

Organism

Reference

Nitrate Reductase (Nap)

Nitrate

27.885

0.47

Escherichia coli

(5)

Nitrite Reductase (Nfr)

Nitrite

46.14

0.022

Escherichia coli

(6)

Nitrite Reductase (Nir)

Nitrite

0.465

0.4

Escherichia coli

(7)



Parameter

Description

Value

Units

Reference

Copy Number in E.coli

300

Copy Number per Cell

Part Registry

Ptrc Promoter Strength

0.00003156

Polymerase per min

(10)(11)(12)

Degradation Rate of mRNA in E.coli

0.102

min-1

(8)

Degradation Rate of Enzyme in E.coli

0.0348

min-1

(8)

Translation rate in E.coli

720~1260

Amino Acids/min

(9)

Avogadaros' Number

6.02*

mmole-1

N/A

Cell Volume of E.coli

6.5*

liter

(18)

Translation rate of Nap

0.763

Number of mRNA/min

Estimated

Translation rate of Nir

0.96

Number of mRNA/min

Estimated

Translation rate of Nor

1.668

Number of mRNA/min

Estimated

Translation rate of Nos

1.602

Number of mRNA/min

Estimated

Parameter

Description

Value

Units

Reference

Copy Number in E.coli

300

Copy Number per Cell

Part Registry

Ptrc Promoter Strength

0.00003156

Polymerase per min

(8)(9)(10)

Degradation Rate of mRNA in E.coli

0.102

min-1

(11)

Degradation Rate of Enzyme in E.coli

0.0348

min-1

(11)

Translation rate in E.coli

720~1260

Amino Acids/min

(12)

Avogadaros' Number

6.02*

mmole-1

N/A

Cell Volume of E.coli

6.5*

liter

(13)

Translation rate of Nap

0.763

Number of mRNA/min

Estimated

Translation rate of Nir

0.96

Number of mRNA/min

Estimated

Translation rate of Nor

1.668

Number of mRNA/min

Estimated

Translation rate of Nos

1.602

Number of mRNA/min

Estimated


Reference

[1]Andrew J. GATES, David J. RICHARDSON, Julea N. BUTT(2008) Voltammetric characterization of the aerobic energy-dissipating nitrate reductase of Paracoccus pantotrophus : exploring the activity of a redox-balancing enzyme as a f unction of electrochemical potential. Biochem. J. (2008) 409, 159–168

[2]Serena Rinaldo, Francesca Cutruzzolà(2007) Nitrite Reductases in Denitrification. Biology of the Nitrogen Cycle 37-55

[3]Naoki Toritsuka, Hirofumi Shoun, Udai P. Singh, Sam-Yong Park , Tetsutaro Iizuka, Yoshitsugu Shiro(1997) Functional and structural comparison of nitric oxide reductases from denitrifying fungi Cylindrocarpon tonkinense and Fusarium oxysporum. Biochimica et Biophysica Acta 1338 1997 93–99

[4]Stuart W. Snyder, Thomas C. Hollocher(1987) Purification and some characteristics of  nitrous oxide reductase from Paracoccus denitrificans. The Journal of Biology Chemistry VOl. 262, No.14. Issue of May 15. , pp. 6515-6525

[5] Robert A. LAZZARINI, Daniel E. Atkinson(1961) A Triphosphopyridine Nucleotide-specific Nitrite Reductase from Escherichia coli. The Journal of Biology Chemistry VOl. 236, No.12. December

[6] Michael W. W. AdamsS, Leonard E. Mortenson(1982) The Effect of Cyanide and Ferricyanide on the Activity of the Dissimilatory Nitrate Reductase of Escherichia coli. The Journal of Biology Chemistry VOl. 257, No.4. Issue of February 25, pp. 1791-1799

[7] Lewis M. Siegel, David C. Rueger, Michael J. Barber, Rick J. Krueger(1982) Escherichia coli Sulfite Reductase Hemoprotein Subuni. The Journal of Biology Chemistry VOl. 257, No.11. Issue of June 10, pp. 6343-6350

[8] Hsin-Ho Huang, Daniel Camsund, Peter Lindblad and Thorsten Heidorn(2010) Design and characterization of molecular tools for a Synthetic Biology approach towards developing cyanobacterial biotechnology. Nucleic Acids Research, Vol. 38, No. 8 2577–2593

[9] Michael Brunner, Hermann Bujard(1987) Promoter recognition and promoter strength in the Escherichia coli system. The EMBO Journal vol.6 no.10 pp.3139-3144

[10]Thomas A . Clarke , Paul C. Mills, Susie R. Poock,bJulea N. Butt, Myles R. Cheesman, Jeffrey A. Cole, Jay C. D. Hinton, Andrew M. Hemmings, Gemma Kemp, Christopher A . G . So¨derberg, Stephen Spiro, Jessica Van Wonderen, David J. Richardson(2008)Escherichia coli Cytochrome c Nitrite Reductase NrfA. Methods in Enzymology, Vol. 437 pp.64-77

[11] Kmalendu Nath, Arthur L. Koch(1971) Protein Degradation in Escherichia coli. The Journal of Biology Chemistry VOl. 246, No.22. Issue of November 25, pp. 6956-6967

[12]Thomas A . Clarke , Paul C. Mills, Susie R. Poock,bJulea N. Butt, Myles R. Cheesman, Jeffrey A. Cole, Jay C. D. Hinton, Andrew M. Hemmings, Gemma Kemp, Christopher A . G . So¨derberg, Stephen Spiro, Jessica Van Wonderen, David J. Richardson(2008)Escherichia coli Cytochrome c Nitrite Reductase NrfA. Methods in Enzymology, Vol. 437 pp.64-77

[13] Cell Volume Increase in Escherichia coli after Shifts to Richer Media, H. E. KUBITSCHEK ,Biological and Medical Research Division, Argonne National Laboratory,9700 South Cass Avenue, Argonne, Illinois 60439