Difference between revisions of "Part:BBa K1150002"
(→‎Sequence and Features)
 
(42 intermediate revisions by 2 users not shown)
Line 2: Line 2:
 
<partinfo>BBa_K1150002 short</partinfo>
 
<partinfo>BBa_K1150002 short</partinfo>
  
−
{| style="color:black" cellpadding="6" cellspacing="1" border="2" align="right"
+
{| style="color:black" cellpadding="7" cellspacing="1" border="1" align="right"
 
! colspan="2" style="background:#FFBF00;"|KRAB
 
! colspan="2" style="background:#FFBF00;"|KRAB
 
|-
 
|-
Line 10: Line 10:
 
|'''Use in'''
 
|'''Use in'''
 
|Mammalian cells
 
|Mammalian cells
 +
|-
 +
|'''Organism'''
 +
|<i>Homo sapiens</i>
 
|-
 
|-
 
|'''RFC standard'''
 
|'''RFC standard'''
Line 15: Line 18:
 
|-
 
|-
 
|'''Backbone'''
 
|'''Backbone'''
−
|pSB1C3<br>
+
|pSB1C3
−
|-
+
−
|'''Organism'''
+
−
|Homo sapiens
+
 
|-
 
|-
 
|'''Source'''
 
|'''Source'''
−
|Konrad Müller, pKM102
+
|Konrad Müller
 
|-
 
|-
 
|'''Submitted by'''
 
|'''Submitted by'''
Line 27: Line 27:
 
|}
 
|}
  
−
Krüppel-associated Box repressor domains - commonly termed as KRAB - are highly conserved polypeptide motifs and were first functionally characterized in 1991 (<i>Rosati et al.</i>, 1991). As they constitute about one third of all human zinc finger transcription factors, key regulatory features in higher eukaryotic transcriptomics are suggested (<i>Witzgall et al.</i>, 1994). Even in terms of tetrapod evolution, the role of their great abundance has been extensively discussed (<i>Birtle & Ponting</i>, 2006). Even though KRAB minimal domains are usually no longer than ~ 50-75 amino acids, their mechanism of function remains complex. <br>
+
[[File:KRAB_Figure_Freiburg.jpg|210px|thumb|left|<b>Fig. 1</b> Structural Mechanism of KRAB, as suggested <i>Urrutia, R., 2003</i>.]]
  
−
[[File:KRAB_Figure_Freiburg.jpg|300px|thumb|center|<b>Fig. 1</b> Structural Mechanism of KRAB Transcription Factors, as suggested by <i>Urrutia, R. (2003)</i>.]]
+
<div align="justify"; margin-right:10px><br>Krüppel-associated Box repressor domains - commonly termed as KRAB - are highly conserved polypeptide motifs and were first functionally characterized in 1991 (<i>Rosati et al.</i>, 1991). As they constitute about one third of all human zinc finger transcription factors, key regulatory features in higher eukaryotic transcrip-<br>tomics are suggested (<i>Witzgall et al.</i>, 1994). Even in terms of tetrapod evolution, the role of their great abundance has been extensively discussed (<i>Birtle</i>, 2006). Even though KRAB minimal domains are usually no longer than 50-75 amino acids, their mechanism of function remains complex. </div><br>
  
−
<br> Common biochemical models suggest a key role in epigenetic silencing, by recruiting a scaffold of diverse proteins - amongst others histone deacetylases and histone methyltransferases (<i>Urrutia</i>, 2003). Til date in 2013, KRAB repressor domains were attached to several DNA binding proteins such as tetR, TAL effectors and [http://2013.igem.org/Team:Freiburg/Project/effector#repression dCas9] - thereby efficiently silencing gene expression downstream of desired target promoters.
+
<div align="justify"; margin-right:10px><br> Common biochemical models suggest a key role in epigenetic silencing, by recruiting a scaffold of diverse proteins - amongst others histone deacetylases and histone methyltransferases (<i>Urrutia</i>, 2003). Til date in 2013, KRAB repressor domains were attached to several DNA binding proteins such as tetR, TAL effec-<br>tors and [http://2013.igem.org/Team:Freiburg/Project/effector#repression dCas9] - thereby efficiently silencing gene expression downstream of desired target promoters. <br><br> The latter combinatorial attempt was conducted twice by Team Freiburg 2013, which resulted in two composite parts - [https://parts.igem.org/wiki/index.php?title=Part:BBa_K1150021 SV40-dCas9-KRAB] and [https://parts.igem.org/wiki/index.php?title=Part:BBa_K1150022 CMV-dCas9-KRAB].<br><br>
 +
</div>
  
−
 
−
 
−
 
−
<!-- Uncomment this to enable Functional Parameter display
 
−
==Usage and Biology==
 
−
<!-- -->
 
−
 
−
<!-- -->
 
 
<span class='h3bb'>
 
<span class='h3bb'>
 
==Sequence and Features==
 
==Sequence and Features==
 
</span>
 
</span>
 
<partinfo>BBa_K1150002 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K1150002 SequenceAndFeatures</partinfo>
 +
<br>
 +
<html><!--- Please copy this table containing parameters for BBa_ at the end of the parametrs section ahead of the references. ---><style type="text/css">table#AutoAnnotator {border:1px solid black; width:100%; border-collapse:collapse;} th#AutoAnnotatorHeader { border:1px solid black; width:100%; background-color: rgb(221, 221, 221);} td.AutoAnnotator1col { width:100%; border:1px solid black; } span.AutoAnnotatorSequence { font-family:'Courier New', Arial; } td.AutoAnnotatorSeqNum { text-align:right; width:2%; } td.AutoAnnotatorSeqSeq { width:98% } td.AutoAnnotatorSeqFeat1 { width:3% } td.AutoAnnotatorSeqFeat2a { width:27% } td.AutoAnnotatorSeqFeat2b { width:97% } td.AutoAnnotatorSeqFeat3 { width:70% } table.AutoAnnotatorNoBorder { border:0px; width:100%; border-collapse:collapse; } table.AutoAnnotatorWithBorder { border:1px solid black; width:100%; border-collapse:collapse; } td.AutoAnnotatorOuterAmino { border:0px solid black; width:20% } td.AutoAnnotatorInnerAmino { border:1px solid black; width:50% } td.AutoAnnotatorAminoCountingOuter { border:1px solid black; width:40%;  } td.AutoAnnotatorBiochemParOuter { border:1px solid black; width:60%; } td.AutoAnnotatorAminoCountingInner1 { width: 7.5% } td.AutoAnnotatorAminoCountingInner2 { width:62.5% } td.AutoAnnotatorAminoCountingInner3 { width:30% } td.AutoAnnotatorBiochemParInner1 { width: 5% } td.AutoAnnotatorBiochemParInner2 { width:55% } td.AutoAnnotatorBiochemParInner3 { width:40% } td.AutoAnnotatorCodonUsage1 { width: 3% } td.AutoAnnotatorCodonUsage2 { width:14.2% } td.AutoAnnotatorCodonUsage3 { width:13.8% } td.AutoAnnotatorAlignment1 { width: 3% } td.AutoAnnotatorAlignment2 { width: 10% } td.AutoAnnotatorAlignment3 { width: 87% } td.AutoAnnotatorLocalizationOuter {border:1px solid black; width:40%} td.AutoAnnotatorGOOuter {border:1px solid black; width:60%} td.AutoAnnotatorLocalization1 { width: 7.5% } td.AutoAnnotatorLocalization2 { width: 22.5% } td.AutoAnnotatorLocalization3 { width: 70% } td.AutoAnnotatorGO1 { width: 5% } td.AutoAnnotatorGO2 { width: 35% } td.AutoAnnotatorGO3 { width: 60% } td.AutoAnnotatorPredFeat1 { width:3% } td.AutoAnnotatorPredFeat2a { width:27% } td.AutoAnnotatorPredFeat3 { width:70% } div.AutoAnnotator_trans { position:absolute; background:rgb(11,140,143); background-color:rgba(11,140,143, 0.8); height:5px; top:100px; } div.AutoAnnotator_sec_helix { position:absolute; background:rgb(102,0,102); background-color:rgba(102,0,102, 0.8); height:5px; top:110px; } div.AutoAnnotator_sec_strand { position:absolute; background:rgb(245,170,26); background-color:rgba(245,170,26, 1); height:5px; top:110px; } div.AutoAnnotator_acc_buried { position:absolute; background:rgb(89,168,15); background-color:rgba(89,168,15, 0.8); height:5px; top:120px; } div.AutoAnnotator_acc_exposed { position:absolute; background:rgb(0, 0, 255); background-color:rgba(0, 0, 255, 0.8); height:5px; top:120px; } div.AutoAnnotator_dis { position:absolute; text-align:center; font-family:Arial,Helvetica,sans-serif; background:rgb(255, 200, 0); background-color:rgba(255, 200, 0, 1); height:16px; width:16px; top:80px; border-radius:50%; } </style><div id='AutoAnnotator_container_1381279420446'><table id="AutoAnnotator"><tr><!-- Time stamp in ms since 1/1/1970 1381279420446 --><th id="AutoAnnotatorHeader" colspan="2">Protein data table for BioBrick <a href="https://parts.igem.org/wiki/index.php?title=Part:BBa_K1150002<!------------------------Enter BioBrick number here------------------------>">BBa_K1150002<!------------------------Enter BioBrick number here------------------------></a> automatically created by the <a href="http://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">BioBrick-AutoAnnotator</a> version 1.0</th></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Nucleotide sequence</strong> in <strong>RFC 25 N-Part</strong> using the stop codon in the suffix, so ACCGGT was added (in italics) to the 3' end: (underlined part encodes the protein)<br><span class="AutoAnnotatorSequence">&nbsp;<u>ATGGATGCT&nbsp;...&nbsp;GATCTCTGG<i>ACCGGT</i></u></span><br>&nbsp;<strong>ORF</strong> from nucleotide position 1 to 372 (excluding stop-codon)</td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Amino acid sequence:</strong> (RFC 25 scars in shown in bold, other sequence features underlined; both given below)<br><span class="AutoAnnotatorSequence"><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorSeqNum">1&nbsp;<br>101&nbsp;</td><td class="AutoAnnotatorSeqSeq">MDAKSLTAWSRTLVTFKDVFVDFTREEWKLLDTAQQIVYRNVMLENYKNLVSLGYQLTKPDVILRLEKGEEPWLVEREIHQETHPDSETAFEIKSSVSSR<br>SIFKDKQSCDIKMEGMARNDLWTG*</td></tr></table></span></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Sequence features:</strong> (with their position in the amino acid sequence, see the <a href="http://2013.igem.org/Team:TU-Munich/Results/Software/FeatureList">list of supported features</a>)<table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorSeqFeat1"></td><td class="AutoAnnotatorSeqFeat2b">None of the supported features appeared in the sequence</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Amino acid composition:</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Ala (A)</td><td class="AutoAnnotatorInnerAmino">5 (4.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Arg (R)</td><td class="AutoAnnotatorInnerAmino">7 (5.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asn (N)</td><td class="AutoAnnotatorInnerAmino">4 (3.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Asp (D)</td><td class="AutoAnnotatorInnerAmino">9 (7.3%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Cys (C)</td><td class="AutoAnnotatorInnerAmino">1 (0.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gln (Q)</td><td class="AutoAnnotatorInnerAmino">5 (4.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Glu (E)</td><td class="AutoAnnotatorInnerAmino">12 (9.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Gly (G)</td><td class="AutoAnnotatorInnerAmino">4 (3.2%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">His (H)</td><td class="AutoAnnotatorInnerAmino">2 (1.6%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ile (I)</td><td class="AutoAnnotatorInnerAmino">6 (4.8%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Leu (L)</td><td class="AutoAnnotatorInnerAmino">12 (9.7%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Lys (K)</td><td class="AutoAnnotatorInnerAmino">10 (8.1%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Met (M)</td><td class="AutoAnnotatorInnerAmino">4 (3.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Phe (F)</td><td class="AutoAnnotatorInnerAmino">5 (4.0%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Pro (P)</td><td class="AutoAnnotatorInnerAmino">3 (2.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Ser (S)</td><td class="AutoAnnotatorInnerAmino">10 (8.1%)</td></tr></table></td><td class="AutoAnnotatorOuterAmino"><table class="AutoAnnotatorWithBorder"><tr><td class="AutoAnnotatorInnerAmino">Thr (T)</td><td class="AutoAnnotatorInnerAmino">9 (7.3%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Trp (W)</td><td class="AutoAnnotatorInnerAmino">4 (3.2%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Tyr (Y)</td><td class="AutoAnnotatorInnerAmino">3 (2.4%)</td></tr><tr><td class="AutoAnnotatorInnerAmino">Val (V)</td><td class="AutoAnnotatorInnerAmino">9 (7.3%)</td></tr></table></td></tr></table></td></tr><tr><td class="AutoAnnotatorAminoCountingOuter"><strong>Amino acid counting</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Total number:</td><td class="AutoAnnotatorAminoCountingInner3">124</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Positively charged (Arg+Lys):</td><td class="AutoAnnotatorAminoCountingInner3">17 (13.7%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Negatively charged (Asp+Glu):</td><td class="AutoAnnotatorAminoCountingInner3">21 (16.9%)</td></tr><tr><td class="AutoAnnotatorAminoCountingInner1"></td><td class="AutoAnnotatorAminoCountingInner2">Aromatic (Phe+His+Try+Tyr):</td><td class="AutoAnnotatorAminoCountingInner3">14 (11.3%)</td></tr></table></td><td class="AutoAnnotatorBiochemParOuter"><strong>Biochemical parameters</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Atomic composition:</td><td class="AutoAnnotatorBiochemParInner3">C<sub>647</sub>H<sub>1016</sub>N<sub>172</sub>O<sub>198</sub>S<sub>5</sub></td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Molecular mass [Da]:</td><td class="AutoAnnotatorBiochemParInner3">14532.5</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Theoretical pI:</td><td class="AutoAnnotatorBiochemParInner3">5.22</td></tr><tr><td class="AutoAnnotatorBiochemParInner1"></td><td class="AutoAnnotatorBiochemParInner2">Extinction coefficient at 280 nm [M<sup>-1</sup> cm<sup>-1</sup>]:</td><td class="AutoAnnotatorBiochemParInner3">26470 / 26533 (all Cys red/ox)</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges</strong>&nbsp;<input type='button' id='hydrophobicity_charge_button' onclick='show_or_hide_plot_1381279420446()' value='Show'><span id="hydrophobicity_charge_explanation"></span><div id="hydrophobicity_charge_container" style='display:none'><div id="hydrophobicity_charge_placeholder0" style="width:100%;height:150px"></div></div></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Codon usage</strong><table class="AutoAnnotatorNoBorder"><tr><td class="AutoAnnotatorCodonUsage1"></td><td class="AutoAnnotatorCodonUsage2">Organism:</td><td class="AutoAnnotatorCodonUsage3"><i>E. coli</i></td><td class="AutoAnnotatorCodonUsage3"><i>B. subtilis</i></td><td class="AutoAnnotatorCodonUsage3"><i>S. cerevisiae</i></td><td class="AutoAnnotatorCodonUsage3"><i>A. thaliana</i></td><td class="AutoAnnotatorCodonUsage3"><i>P. patens</i></td><td class="AutoAnnotatorCodonUsage3">Mammals</td></tr><tr><td class="AutoAnnotatorCodonUsage1"></td><td class="AutoAnnotatorCodonUsage2">Codon quality (<a href="http://en.wikipedia.org/wiki/Codon_Adaptation_Index">CAI</a>):</td><td class="AutoAnnotatorCodonUsage3">good (0.70)</td><td class="AutoAnnotatorCodonUsage3">good (0.70)</td><td class="AutoAnnotatorCodonUsage3">good (0.65)</td><td class="AutoAnnotatorCodonUsage3">good (0.76)</td><td class="AutoAnnotatorCodonUsage3">excellent (0.85)</td><td class="AutoAnnotatorCodonUsage3">good (0.79)</td></tr></table></td></tr><tr><td class="AutoAnnotator1col" colspan="2"><strong>Alignments</strong> (obtained from <a href='http://predictprotein.org'>PredictProtein.org</a>)<br>&nbsp;&nbsp;&nbsp;There were no alignments for this protein in the data base. The BLAST search was initialized and should be ready in a few hours.</td></tr><tr><th id='AutoAnnotatorHeader' colspan="2"><strong>Predictions</strong> (obtained from <a href='http://predictprotein.org'>PredictProtein.org</a>)</th></tr><tr><td class="AutoAnnotator1col" colspan="2">&nbsp;&nbsp;&nbsp;There were no predictions for this protein in the data base. The prediction was initialized and should be ready in a few hours.</td><tr><td class="AutoAnnotator1col" colspan="2"> The BioBrick-AutoAnnotator was created by <a href="http://2013.igem.org/Team:TU-Munich">TU-Munich 2013</a> iGEM team. For more information please see the <a href="http://2013.igem.org/Team:TU-Munich/Results/Software">documentation</a>.<br>If you have any questions, comments or suggestions, please leave us a <a href="http://2013.igem.org/Team:TU-Munich/Results/AutoAnnotator">comment</a>.</td></tr></table></div><br><!-- IMPORTANT: DON'T REMOVE THIS LINE, OTHERWISE NOT SUPPORTED FOR IE BEFORE 9 --><!--[if lte IE 8]><script language="javascript" type="text/javascript" src="excanvas.min.js"></script><![endif]--><script type='text/javascript' src='http://code.jquery.com/jquery-1.10.0.min.js'></script><script type='text/javascript' src='http://2013.igem.org/Team:TU-Munich/Flot.js?action=raw&ctype=text/js'></script><script>function show_or_hide_plot_1381279420446(){hydrophobicity_datapoints = [[2.5,-0.90],[3.5,-0.52],[4.5,0.04],[5.5,0.04],[6.5,0.64],[7.5,0.64],[8.5,-1.02],[9.5,-1.02],[10.5,-0.62],[11.5,0.40],[12.5,0.42],[13.5,1.88],[14.5,1.24],[15.5,-0.22],[16.5,-0.22],[17.5,0.48],[18.5,0.76],[19.5,0.84],[20.5,2.10],[21.5,1.12],[22.5,-0.34],[23.5,-1.88],[24.5,-1.88],[25.5,-2.62],[26.5,-3.26],[27.5,-1.60],[28.5,-0.14],[29.5,-0.14],[30.5,-0.10],[31.5,1.04],[32.5,-0.42],[33.5,-1.88],[34.5,-0.28],[35.5,0.70],[36.5,0.08],[37.5,-0.12],[38.5,-0.12],[39.5,-0.18],[40.5,-0.64],[41.5,0.38],[42.5,0.58],[43.5,0.58],[44.5,-0.52],[45.5,-1.68],[46.5,-3.14],[47.5,-1.68],[48.5,-0.14],[49.5,-0.04],[50.5,1.50],[51.5,2.12],[52.5,1.10],[53.5,-0.44],[54.5,0.48],[55.5,-0.42],[56.5,-1.12],[57.5,-1.18],[58.5,-1.18],[59.5,-1.10],[60.5,-0.06],[61.5,1.48],[62.5,0.90],[63.5,2.36],[64.5,0.82],[65.5,-0.86],[66.5,-1.70],[67.5,-1.50],[68.5,-2.96],[69.5,-2.58],[70.5,-1.98],[71.5,-1.14],[72.5,0.40],[73.5,0.40],[74.5,-0.18],[75.5,-0.70],[76.5,-0.56],[77.5,-2.04],[78.5,-2.04],[79.5,-1.84],[80.5,-1.28],[81.5,-2.82],[82.5,-2.50],[83.5,-2.50],[84.5,-1.96],[85.5,-2.52],[86.5,-2.02],[87.5,-1.34],[88.5,-0.08],[89.5,-0.62],[90.5,0.98],[91.5,0.34],[92.5,-0.18],[93.5,-0.90],[94.5,0.64],[95.5,-0.42],[96.5,0.20],[97.5,-0.54],[98.5,-0.54],[99.5,-0.48],[100.5,0.24],[101.5,-0.38],[102.5,-0.18],[103.5,-0.80],[104.5,-2.40],[105.5,-3.12],[106.5,-1.84],[107.5,-1.84],[108.5,-0.16],[109.5,-0.24],[110.5,0.30],[111.5,-0.90],[112.5,-0.28],[113.5,-0.80],[114.5,0.34],[115.5,-0.94],[116.5,-0.94],[117.5,-1.56],[118.5,-1.18],[119.5,-1.72],[120.5,-0.96],[121.5,-0.34]];charge_datapoints = [[2.5,0.00],[3.5,0.00],[4.5,0.20],[5.5,0.20],[6.5,0.00],[7.5,0.00],[8.5,0.20],[9.5,0.20],[10.5,0.20],[11.5,0.20],[12.5,0.20],[13.5,0.00],[14.5,0.20],[15.5,0.00],[16.5,0.00],[17.5,0.00],[18.5,0.00],[19.5,-0.40],[20.5,-0.20],[21.5,-0.20],[22.5,0.00],[23.5,-0.20],[24.5,-0.20],[25.5,-0.20],[26.5,0.00],[27.5,-0.20],[28.5,0.00],[29.5,0.00],[30.5,0.00],[31.5,-0.20],[32.5,-0.20],[33.5,-0.20],[34.5,0.00],[35.5,0.00],[36.5,0.00],[37.5,0.20],[38.5,0.20],[39.5,0.20],[40.5,0.20],[41.5,0.20],[42.5,-0.20],[43.5,-0.20],[44.5,-0.20],[45.5,0.00],[46.5,0.00],[47.5,0.20],[48.5,0.20],[49.5,0.20],[50.5,0.00],[51.5,0.00],[52.5,0.00],[53.5,0.00],[54.5,0.00],[55.5,0.00],[56.5,0.20],[57.5,0.20],[58.5,0.00],[59.5,0.00],[60.5,0.00],[61.5,-0.20],[62.5,0.00],[63.5,0.20],[64.5,0.00],[65.5,0.20],[66.5,0.20],[67.5,-0.20],[68.5,-0.40],[69.5,-0.20],[70.5,-0.40],[71.5,-0.40],[72.5,-0.20],[73.5,-0.20],[74.5,0.00],[75.5,-0.20],[76.5,-0.20],[77.5,-0.10],[78.5,0.10],[79.5,-0.30],[80.5,-0.10],[81.5,-0.00],[82.5,-0.10],[83.5,-0.30],[84.5,-0.10],[85.5,-0.30],[86.5,-0.40],[87.5,-0.40],[88.5,-0.20],[89.5,-0.40],[90.5,-0.20],[91.5,0.00],[92.5,0.00],[93.5,0.00],[94.5,0.20],[95.5,0.20],[96.5,0.00],[97.5,0.20],[98.5,0.20],[99.5,0.20],[100.5,0.20],[101.5,0.40],[102.5,0.00],[103.5,0.20],[104.5,0.20],[105.5,0.20],[106.5,0.00],[107.5,0.00],[108.5,-0.20],[109.5,0.00],[110.5,0.00],[111.5,-0.20],[112.5,0.00],[113.5,0.00],[114.5,-0.20],[115.5,0.00],[116.5,0.20],[117.5,0.00],[118.5,0.00],[119.5,0.00],[120.5,-0.20],[121.5,-0.20]];dis_datapoints = undefined;trans_datapoints = undefined;sec_helix_datapoints = undefined;sec_strand_datapoints = undefined;acc_exposed_datapoints = undefined;acc_buried_datapoints = undefined;flot_plot_options = []; flot_plot_options[0] = {grid: {borderWidth: {top: 0,right: 0,bottom: 0,left: 0}},legend: {show: false},xaxes: [{show: true,min: 0,max: 200,ticks: [[0.5, '1'], [24.5, '25'], [49.5, '50'], [74.5, '75'], [99.5, '100'], [124.5, '125'], [149.5, '150'], [174.5, '175'], [199.5, '200']],tickLength: -5}],yaxes: [{show: true,ticks: [[0, '0'], [4.5,'hydro-<br>phobic&nbsp;&nbsp;'], [-4.5,'hydro-<br>philic&nbsp;&nbsp;']],min: -4.5,max: +4.5,font: {size: 12,lineHeight: 14,style: 'italic',weight: 'bold',family: 'sans-serif',variant: 'small-caps',color: 'rgba(100,149,237,1)'}},{show: true,ticks: [[0, ''], [1,'positive<br>&nbsp;charge'], [-1,'negative<br>&nbsp;charge']],position: 'right',min: -1,max: 1,font: {size: 12,lineHeight: 14,style: 'italic',weight: 'bold',family: 'sans-serif',variant: 'small-caps',color: 'rgba(255,99,71,1)'}}]};number_of_plots = 1;for ( plot_num = 1 ; plot_num < number_of_plots ; plot_num ++){flot_plot_options[plot_num] = $.extend(true, {} ,flot_plot_options[0]);flot_plot_options[plot_num].xaxes = [{min: plot_num*200,max: (plot_num + 1)*200,ticks: [ [plot_num*200 +  0.5, (plot_num*200 +  1).toString()], [plot_num*200 +  24.5, (plot_num*200 +  25).toString()], [plot_num*200 +  49.5, (plot_num*200 +  50).toString()], [plot_num*200 +  74.5, (plot_num*200 +  75).toString()], [plot_num*200 +  99.5, (plot_num*200 + 100).toString()], [plot_num*200 + 124.5, (plot_num*200 + 125).toString()], [plot_num*200 + 149.5, (plot_num*200 + 150).toString()], [plot_num*200 + 174.5, (plot_num*200 + 175).toString()], [plot_num*200 + 199.5, (plot_num*200 + 200).toString()] ],tickLength: -5}];};try {if( $('#AutoAnnotator_container_1381279420446 #hydrophobicity_charge_button').val() =='Show' ){$('#AutoAnnotator_container_1381279420446 #hydrophobicity_charge_container').css('display','block');$('#AutoAnnotator_container_1381279420446 #hydrophobicity_charge_button').val('Hide');var description_html = '<div id=\'AutoAnnotator_plot_selectors\'>';description_html = description_html + '<br>&nbsp;<input type=\'checkbox\' id=\'hydrophobicity_checkbox\' checked=\'checked\'>&nbsp;Moving average over 5 amino acids for hydrophobicity (<img src=\'https://static.igem.org/mediawiki/2013/e/e9/TUM13_hydrophobicity_icon.png\' alt=\'blue graph\' height=\'10\'></img>)';description_html = description_html + '<br>&nbsp;<input type=\'checkbox\' id=\'charge_checkbox\' checked=\'checked\'>&nbsp;Moving average over 5 amino acids for charge (<img src=\'https://static.igem.org/mediawiki/2013/3/3e/TUM13_charge_icon.png\' alt=\'red graph\' height=\'10\'></img>)';description_html = description_html + '<br>&nbsp;<input type=\'checkbox\' id=\'dis_checkbox\' checked=\'checked\'>&nbsp;Predicted disulfid bridges (<img src=\'https://static.igem.org/mediawiki/2013/2/28/TUM13_dis_icon.png\' alt=\'yellow circle\' height=\'10\'></img>) with the number of the bridge in the center';description_html = description_html + '<br>&nbsp;<input type=\'checkbox\' id=\'trans_checkbox\' checked=\'checked\'>&nbsp;Predicted transmembrane helices (<img src=\'https://static.igem.org/mediawiki/2013/7/78/TUM13_trans_icon.png\' alt=\'turquois bars\' height=\'10\'></img>)';description_html = description_html + '<br>&nbsp;<input type=\'checkbox\' id=\'sec_checkbox\' checked=\'checked\'>&nbsp;Predicted secondary structure: Helices (<img src=\'https://static.igem.org/mediawiki/2013/b/bf/TUM13_helix_icon.png\' alt=\'violet bars\' height=\'10\'></img>) and beta-strands (<img src=\'https://static.igem.org/mediawiki/2013/b/bf/TUM13_strand_icon.png\' alt=\'yellow bars\' height=\'10\'></img>)';description_html = description_html + '<br>&nbsp;<input type=\'checkbox\' id=\'acc_checkbox\' checked=\'checked\'>&nbsp;Predicted solvent accessability: Exposed (<img src=\'https://static.igem.org/mediawiki/2013/1/16/TUM13_exposed_icon.png\' alt=\'blue bars\' height=\'10\'></img>) and buried (<img src=\'https://static.igem.org/mediawiki/2013/0/0b/TUM13_buried_icon.png\' alt=\'green bars\' height=\'10\'></img>) residues';description_html = description_html + '<br></div>';$('#AutoAnnotator_container_1381279420446 #hydrophobicity_charge_explanation').html(description_html);plot_according_to_selectors_1381279420446();$('#AutoAnnotator_container_1381279420446 #AutoAnnotator_plot_selectors').find('input').click(plot_according_to_selectors_1381279420446);}else{$('#AutoAnnotator_container_1381279420446 #hydrophobicity_charge_container').css('display','none');$('#AutoAnnotator_container_1381279420446 #hydrophobicity_charge_button').val('Show');$('#AutoAnnotator_container_1381279420446 #hydrophobicity_charge_explanation').html('');}}catch(err){txt='There was an error with the button controlling the visibility of the plot.\n';txt=txt+'The originating error is:\n' + err + '\n\n';alert(txt);}};function plot_according_to_selectors_1381279420446(){try{var plot_datasets = [[],[]];if($('#AutoAnnotator_container_1381279420446 #hydrophobicity_checkbox').prop('checked') == true){plot_datasets[0] = { color: 'rgba(100,149,237,1)',data: hydrophobicity_datapoints,label: 'Hydrophobicity',lines: { show: true, fill: true, fillColor: 'rgba(100,149,237,0.1)' },yaxis: 1};}if($('#AutoAnnotator_container_1381279420446 #charge_checkbox').prop('checked') == true){plot_datasets[1] = {color: 'rgba(255,99,71,1)',data: charge_datapoints,label: 'Charge',lines: { show: true, fill: true, fillColor: 'rgba(255,99,71,0.1)' },yaxis: 2};}for (plot_num = 0 ; plot_num < number_of_plots ; plot_num ++){$.plot('#AutoAnnotator_container_1381279420446 #hydrophobicity_charge_placeholder'+ plot_num.toString(), plot_datasets, flot_plot_options[plot_num] );}var screen_width = $('canvas.flot-base').width(); var pos_of_first_tick = 46;var pos_of_last_tick = screen_width - 51;var tick_diff = (screen_width - 97)/199;if($('#AutoAnnotator_container_1381279420446 #dis_checkbox').prop('checked') == true){for ( j = 0 ; j < dis_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381279420446 #hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_dis\' style=\'left:' + ((pos_of_first_tick - 8 + (dis_datapoints[j][0] - 1)*tick_diff - Math.floor((dis_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px;\'><b>' + (j+1) + '</b></div>');$('#AutoAnnotator_container_1381279420446 #hydrophobicity_charge_placeholder' + Math.floor((dis_datapoints[j][1] - 1)/200) ).append('<div class=\'AutoAnnotator_dis\' style=\'left:' + ((pos_of_first_tick - 8 + (dis_datapoints[j][1] - 1)*tick_diff - Math.floor((dis_datapoints[j][1] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px;\'><b>' + (j+1) + '</b></div>');}}if($('#AutoAnnotator_container_1381279420446 #trans_checkbox').prop('checked') == true){for ( j = 0 ; j < trans_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381279420446 #hydrophobicity_charge_placeholder' + Math.floor((trans_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_trans\' style=\'width:' + (((trans_datapoints[j][1] - trans_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px ;left:' + ((pos_of_first_tick + (trans_datapoints[j][0] - 1.5)*tick_diff - Math.floor((trans_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}}if($('#AutoAnnotator_container_1381279420446 #sec_checkbox').prop('checked') == true){for ( j = 0 ; j < sec_helix_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381279420446 #hydrophobicity_charge_placeholder' + Math.floor((sec_helix_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_sec_helix\' style=\'width:' + (((sec_helix_datapoints[j][1] - sec_helix_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (sec_helix_datapoints[j][0] - 1.5)*tick_diff - Math.floor((sec_helix_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}for ( j = 0 ; j < sec_strand_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381279420446 #hydrophobicity_charge_placeholder' + Math.floor((sec_strand_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_sec_strand\' style=\'width:' + (((sec_strand_datapoints[j][1] - sec_strand_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (sec_strand_datapoints[j][0] - 1.5)*tick_diff - Math.floor((sec_strand_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}}if($('#AutoAnnotator_container_1381279420446 #acc_checkbox').prop('checked') == true){for ( j = 0 ; j < acc_buried_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381279420446 #hydrophobicity_charge_placeholder' + Math.floor((acc_buried_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_acc_buried\' style=\'width:' + (((acc_buried_datapoints[j][1] - acc_buried_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (acc_buried_datapoints[j][0] - 1.5)*tick_diff - Math.floor((acc_buried_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}for ( j = 0 ; j < acc_exposed_datapoints.length ; j++ ){$('#AutoAnnotator_container_1381279420446 #hydrophobicity_charge_placeholder' + Math.floor((acc_exposed_datapoints[j][0] - 1)/200) ).append('<div class=\'AutoAnnotator_acc_exposed\' style=\'width:' + (((acc_exposed_datapoints[j][1] - acc_exposed_datapoints[j][0] + 1)*tick_diff).toFixed(0)).toString() + 'px; left:' + ((pos_of_first_tick + (acc_exposed_datapoints[j][0] - 1.5)*tick_diff - Math.floor((acc_exposed_datapoints[j][0] - 1)/200)*200*tick_diff).toFixed(0)).toString() + 'px\'></div>');}}}catch(err){txt='There was an error while drawing the selected elements for the plot.\n';txt=txt+'The originating error is:\n' + err + '\n\n';throw(txt);}}</script></html>
  
−
 
+
==References==
−
<!-- Uncomment this to enable Functional Parameter display
+
<small>
−
===Functional Parameters===
+
Rosati, M. <i>et al.</i> (1991). Members of the zinc finger protein gene family sharing a conserved N-terminal module. Nucleic acids research 19, <i>5661-5667</i>. <br>
−
<partinfo>BBa_K1150002 parameters</partinfo>
+
Witzgall, R. <i>et al.</i> (1994). The Krüppel-associated box-A domain of zinc finger proteins mediates transcriptional repression. Proc Nati Acad Sci 91, <i>4514-4518</i>. <br>
−
<!-- -->
+
Birtle, Z. and Ponting, C. (2006). Meisetz and the birth of the KRAB motif. Bioinformatics 22, <i>2841-2845</i>. <br>
−
 
+
Urrutia, R. (2003). KRAB-containing zinc-finger repressor proteins. Genome Biology 4, <i>4:231</i>.</small>
−
==Literature==
+
−
<div id="(1)">(1) Rosati, M. <i>et al.</i> (1991). Members of the zinc finger protein gene family sharing a conserved N-terminal module. Nucleic acids research 19, <i>5661-5667</i>. <br></div>
+
−
<div id="(2)">(2) Witzgall, R. <i>et al.</i> (1994). The Krüppel-associated box-A domain of zinc finger proteins mediates transcriptional repression. Proc Nati Acad Sci 91, <i>4514-4518</i>. <br></div>
+
−
<div id="(3)">(3) Birtle, Z. and Ponting, C. (2006). Meisetz and the birth of the KRAB motif. Bioinformatics 22, <i>2841-2845</i>. <br></div>
+
−
<div id="(4)">(4) Urrutia, R. (2003). KRAB-containing zinc-finger repressor proteins. Genome Biology 4, <i>4:231</i>. <br></div>
+

Latest revision as of 00:44, 9 October 2013

KRAB

KRAB
Function Repressor domain
Use in Mammalian cells
Organism Homo sapiens
RFC standard RFC 25
Backbone pSB1C3
Source Konrad Müller
Submitted by [http://2013.igem.org/Team:Freiburg Freiburg 2013]
Fig. 1 Structural Mechanism of KRAB, as suggested Urrutia, R., 2003.

Krüppel-associated Box repressor domains - commonly termed as KRAB - are highly conserved polypeptide motifs and were first functionally characterized in 1991 (Rosati et al., 1991). As they constitute about one third of all human zinc finger transcription factors, key regulatory features in higher eukaryotic transcrip-
tomics are suggested (Witzgall et al., 1994). Even in terms of tetrapod evolution, the role of their great abundance has been extensively discussed (Birtle, 2006). Even though KRAB minimal domains are usually no longer than 50-75 amino acids, their mechanism of function remains complex.


Common biochemical models suggest a key role in epigenetic silencing, by recruiting a scaffold of diverse proteins - amongst others histone deacetylases and histone methyltransferases (Urrutia, 2003). Til date in 2013, KRAB repressor domains were attached to several DNA binding proteins such as tetR, TAL effec-
tors and [http://2013.igem.org/Team:Freiburg/Project/effector#repression dCas9] - thereby efficiently silencing gene expression downstream of desired target promoters.

The latter combinatorial attempt was conducted twice by Team Freiburg 2013, which resulted in two composite parts - SV40-dCas9-KRAB and CMV-dCas9-KRAB.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 244
    Illegal SapI.rc site found at 208


Protein data table for BioBrick BBa_K1150002 automatically created by the BioBrick-AutoAnnotator version 1.0
Nucleotide sequence in RFC 25 N-Part using the stop codon in the suffix, so ACCGGT was added (in italics) to the 3' end: (underlined part encodes the protein)
 ATGGATGCT ... GATCTCTGGACCGGT
 ORF from nucleotide position 1 to 372 (excluding stop-codon)
Amino acid sequence: (RFC 25 scars in shown in bold, other sequence features underlined; both given below)
1 
101 		MDAKSLTAWSRTLVTFKDVFVDFTREEWKLLDTAQQIVYRNVMLENYKNLVSLGYQLTKPDVILRLEKGEEPWLVEREIHQETHPDSETAFEIKSSVSSR
SIFKDKQSCDIKMEGMARNDLWTG*
Sequence features: (with their position in the amino acid sequence, see the list of supported features)
None of the supported features appeared in the sequence
Amino acid composition:
Ala (A)5 (4.0%)
Arg (R)7 (5.6%)
Asn (N)4 (3.2%)
Asp (D)9 (7.3%)
Cys (C)1 (0.8%)
Gln (Q)5 (4.0%)
Glu (E)12 (9.7%)
Gly (G)4 (3.2%)
His (H)2 (1.6%)
Ile (I)6 (4.8%)
Leu (L)12 (9.7%)
Lys (K)10 (8.1%)
Met (M)4 (3.2%)
Phe (F)5 (4.0%)
Pro (P)3 (2.4%)
Ser (S)10 (8.1%)
Thr (T)9 (7.3%)
Trp (W)4 (3.2%)
Tyr (Y)3 (2.4%)
Val (V)9 (7.3%)
Amino acid counting
Total number:124
Positively charged (Arg+Lys):17 (13.7%)
Negatively charged (Asp+Glu):21 (16.9%)
Aromatic (Phe+His+Try+Tyr):14 (11.3%)
Biochemical parameters
Atomic composition:C647H1016N172O198S5
Molecular mass [Da]:14532.5
Theoretical pI:5.22
Extinction coefficient at 280 nm [M-1 cm-1]:26470 / 26533 (all Cys red/ox)
Plot for hydrophobicity, charge, predicted secondary structure, solvent accessability, transmembrane helices and disulfid bridges 
Codon usage
Organism:E. coliB. subtilisS. cerevisiaeA. thalianaP. patensMammals
Codon quality (CAI):good (0.70)good (0.70)good (0.65)good (0.76)excellent (0.85)good (0.79)
Alignments (obtained from PredictProtein.org)
   There were no alignments for this protein in the data base. The BLAST search was initialized and should be ready in a few hours.
Predictions (obtained from PredictProtein.org)
   There were no predictions for this protein in the data base. The prediction was initialized and should be ready in a few hours.
The BioBrick-AutoAnnotator was created by TU-Munich 2013 iGEM team. For more information please see the documentation.
If you have any questions, comments or suggestions, please leave us a comment.

References

Rosati, M. et al. (1991). Members of the zinc finger protein gene family sharing a conserved N-terminal module. Nucleic acids research 19, 5661-5667.
Witzgall, R. et al. (1994). The Krüppel-associated box-A domain of zinc finger proteins mediates transcriptional repression. Proc Nati Acad Sci 91, 4514-4518.
Birtle, Z. and Ponting, C. (2006). Meisetz and the birth of the KRAB motif. Bioinformatics 22, 2841-2845.
Urrutia, R. (2003). KRAB-containing zinc-finger repressor proteins. Genome Biology 4, 4:231.