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Capping enzyme
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<h2 id="formation-of-the-cap">Formation of the cap</h2> <p>Capping is a three-step process that utilizes the <a href="/facts/Enzymes/DSI1Fh7y">enzymes</a> RNA triphosphatase, guanylyltransferase, and methyltransferase.<a class="footnote-ref" id="fnref:1" href="#fn:1"><sup>1</sup></a><a class="footnote-ref" id="fnref:2" href="#fn:2"><sup>2</sup></a> Through a series of three steps, the cap is added to the first nucleotide's 5' hydroxyl group of the growing <a href="/facts/MRNA/oUL6qxQn">mRNA</a> strand while <a href="/facts/Transcription_(genetics)/bDgp9HDN">transcription</a> is still occurring.<a class="footnote-ref" id="fnref:3" href="#fn:3"><sup>3</sup></a><a class="footnote-ref" id="fnref:4" href="#fn:4"><sup>4</sup></a> First, RNA 5' triphosphatase hydrolyzes the 5' triphosphate group to make diphosphate-RNA. Then, the addition of <a href="/facts/Guanosine_monophosphate/ex8VI4dR">GMP</a> by guanylyltransferase produces the <a href="/facts/Guanosine/P7YVKuzy">guanosine</a> cap. Last, RNA methyltransferase transfers a <a href="/facts/Methyl_group/fkM97EMD">methyl group</a> to the guanosine cap to yield 7-methylguanosine cap that is attached to the 5' end of the transcript.<a class="footnote-ref" id="fnref:5" href="#fn:5"><sup>5</sup></a><a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a><a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a><a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a> These three enzymes, collectively called the capping enzymes, are only able to <a href="/facts/Catalyze/LPBS7TQC">catalyze</a> their respective reactions when attached to RNA polymerase II, an enzyme necessary for the transcription of DNA into pre-mRNA. When this complex of RNA polymerase II and the capping enzymes is achieved, the capping enzymes are able to add the cap to the mRNA while it is produced by RNA polymerase II.<a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> </p> <h2 id="function">Function</h2> <p>Eukaryotic RNA must undergo a series of modifications in order to be exported from the <a href="/facts/Cell_nucleus/D7sFRa3c">nucleus</a> and successfully translated into function proteins, many of which are dependent on mRNA capping, the first mRNA modification to take place.<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a><a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a> 5' capping is essential for mRNA stability, enhancing mRNA processing, mRNA export and translation.<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a><a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a><a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a> After successful capping, an additional phosphorylation event initiates the recruitment of machinery necessary for RNA splicing, a process by which introns are removed to produce a mature mRNA.<a class="footnote-ref" id="fnref:15" href="#fn:15"><sup>15</sup></a> The addition of the cap onto mRNA confers protection to the transcript from exonucleases that degrade unprotected RNA and assist in the nuclear export transport process so that the mRNA can be translated to form proteins.<a class="footnote-ref" id="fnref:16" href="#fn:16"><sup>16</sup></a> The function of the 5' cap is essential to the ultimate expression of the RNA.<a class="footnote-ref" id="fnref:17" href="#fn:17"><sup>17</sup></a> </p> <h2 id="structure">Structure</h2> <p>The capping enzyme is part of the covalent <a href="/facts/Nucleotidyltransferase/IE9v9yLF">nucleotidyl transferases</a> <a href="/facts/Superfamily_(biology)/bPFQpe9A">superfamily</a>, which also includes <a href="/facts/DNA_ligase/gvgKYAJD">DNA ligases</a> and <a href="/facts/RNA_ligase/CNED6Xuh">RNA ligases</a>.<a class="footnote-ref" id="fnref:18" href="#fn:18"><sup>18</sup></a><a class="footnote-ref" id="fnref:19" href="#fn:19"><sup>19</sup></a><a class="footnote-ref" id="fnref:20" href="#fn:20"><sup>20</sup></a><a class="footnote-ref" id="fnref:21" href="#fn:21"><sup>21</sup></a> The enzymes of this superfamily share the following similarities: </p> <ul><li>Conserved regions known as <a href="/facts/Structural_motif/g8EBDBGW">motifs</a> I, II, III, IIIa, IV, V and VI, which are arranged in the same order and similar spacing<a class="footnote-ref" id="fnref:22" href="#fn:22"><sup>22</sup></a><a class="footnote-ref" id="fnref:23" href="#fn:23"><sup>23</sup></a><a class="footnote-ref" id="fnref:24" href="#fn:24"><sup>24</sup></a></li> <li>A <a href="/facts/Lysine/CEetgA9L">lysine</a> containing motif KxDG (motif I)<a class="footnote-ref" id="fnref:25" href="#fn:25"><sup>25</sup></a><a class="footnote-ref" id="fnref:26" href="#fn:26"><sup>26</sup></a></li> <li>A <a href="/facts/Covalent/EzMLf3Pz">covalent</a> lysyl-NMP intermediate<a class="footnote-ref" id="fnref:27" href="#fn:27"><sup>27</sup></a><a class="footnote-ref" id="fnref:28" href="#fn:28"><sup>28</sup></a></li></ul> <p>The capping enzyme is composed of two <a href="/facts/Protein_domain/oUpFcSsl">domains</a>, a nucleotidyl transferase (NTase) domain and a C-terminal oligonucleotide binding (OB) domain.<a class="footnote-ref" id="fnref:29" href="#fn:29"><sup>29</sup></a><a class="footnote-ref" id="fnref:30" href="#fn:30"><sup>30</sup></a> The NTase domain, conserved in capping enzymes, DNA and RNA ligases, is made up 5 motifs, I, III, IIIa, IV and V.<a class="footnote-ref" id="fnref:31" href="#fn:31"><sup>31</sup></a><a class="footnote-ref" id="fnref:32" href="#fn:32"><sup>32</sup></a> Motif I or KxDG is the active site where the covalent (lysyl)-N-GMP intermediate is formed.<a class="footnote-ref" id="fnref:33" href="#fn:33"><sup>33</sup></a><a class="footnote-ref" id="fnref:34" href="#fn:34"><sup>34</sup></a><a class="footnote-ref" id="fnref:35" href="#fn:35"><sup>35</sup></a><a class="footnote-ref" id="fnref:36" href="#fn:36"><sup>36</sup></a> Both the NTase and OB domains undergo conformational changes that assist in the capping reaction.<a class="footnote-ref" id="fnref:37" href="#fn:37"><sup>37</sup></a> </p><p>Capping enzymes are found in the <a href="/facts/Cell_nucleus/D7sFRa3c">nucleus</a> of <a href="/facts/Eukaryote/SkwyPLMA">eukaryotic</a> <a href="/facts/Cell_(biology)/bLM9UQvy">cells</a>.<a class="footnote-ref" id="fnref:38" href="#fn:38"><sup>38</sup></a><a class="footnote-ref" id="fnref:39" href="#fn:39"><sup>39</sup></a> Depending on the organism, the capping enzyme is either a monofunctional or bifunctional <a href="/facts/Peptide/C4ltc7UG">polypeptide</a>.<a class="footnote-ref" id="fnref:40" href="#fn:40"><sup>40</sup></a><a class="footnote-ref" id="fnref:41" href="#fn:41"><sup>41</sup></a> The guanylyltransferases (Ceg1) of <i><a href="/facts/Saccharomyces_cerevisiae/sX9MGFrz">Saccharomyces cerevisiae</a></i> is encoded by the <i>CEG1</i> gene and is composed of 459 amino acids (53-kD).<a class="footnote-ref" id="fnref:42" href="#fn:42"><sup>42</sup></a><a class="footnote-ref" id="fnref:43" href="#fn:43"><sup>43</sup></a> The RNA triphosphatase (Cet1) is a separate 549 amino acid <a href="/facts/Polypeptide/C4ltc7UG">polypeptide</a> (80-kD), encoded by the <i>CET1</i> gene.<a class="footnote-ref" id="fnref:44" href="#fn:44"><sup>44</sup></a><a class="footnote-ref" id="fnref:45" href="#fn:45"><sup>45</sup></a><a class="footnote-ref" id="fnref:46" href="#fn:46"><sup>46</sup></a> The human capping enzyme is an example of a bifunctional polypeptide, which has both triphosphatase (N-terminal) and guanylyltransferase (C-terminal) domains.<a class="footnote-ref" id="fnref:47" href="#fn:47"><sup>47</sup></a><a class="footnote-ref" id="fnref:48" href="#fn:48"><sup>48</sup></a> The human <a href="/facts/MRNA_guanylyltransferase/9IgVYkrj">mRNA guanylyltransferase</a> domain of the capping enzyme is composed of seven <a href="/facts/Alpha_helix/7CESPIYJ">helices</a> and fifteen <a href="/facts/Beta_strand/B6mwwR6H">β strands</a> that are grouped into three, five and seven strands, arranged as antiparallel <a href="/facts/%25CE%2592_sheets/B6mwwR6H">β sheets</a>.<a class="footnote-ref" id="fnref:49" href="#fn:49"><sup>49</sup></a> The enzyme structure has three sub-domains referred to hinge, base and lid.<a class="footnote-ref" id="fnref:50" href="#fn:50"><sup>50</sup></a> The <a href="/facts/Guanosine_triphosphate/NAwoHjTW">GTP</a> binding site is located between the hinge and base domain.<a class="footnote-ref" id="fnref:51" href="#fn:51"><sup>51</sup></a> The lid domain determines the conformation of the <a href="/facts/Active_site/u9ua7rGu">active site</a> cleft, which consists of the GTP binding site, phosphoamide linking lysine and surrounding residues.<a class="footnote-ref" id="fnref:52" href="#fn:52"><sup>52</sup></a> The guanylyltransferase domain is linked to the triphosphatase domain via a 25 amino acid flexible loop structure.<a class="footnote-ref" id="fnref:53" href="#fn:53"><sup>53</sup></a> </p> <h2 id="impact-of-the-enzymes-activity">Impact of the enzyme's activity</h2> <p>Splicing is dependent on the presence of the 7-methylguanosine cap. A defect in splicing can occur as a result of mutation(s) in the <a href="/facts/Guanylyltransferase/Frdobd4s">guanylyltransferase</a>, which can inhibit enzyme activity, preventing the formation of the cap. However the severity of the effect is dependent on the guanylyltransferase mutation.<a class="footnote-ref" id="fnref:54" href="#fn:54"><sup>54</sup></a> Furthermore, the guanylyltransferase relieves transcriptional repression mediated by <a href="/facts/Nasal_embryonic_LHRH_factor/SjJV4aJ7">NELF</a>.<a class="footnote-ref" id="fnref:55" href="#fn:55"><sup>55</sup></a><a class="footnote-ref" id="fnref:56" href="#fn:56"><sup>56</sup></a> NELF together with <a href="/facts/DSIF/jseJHoLY">DSIF</a> prevents transcription elongation.<a class="footnote-ref" id="fnref:57" href="#fn:57"><sup>57</sup></a><a class="footnote-ref" id="fnref:58" href="#fn:58"><sup>58</sup></a> Thus, mutations in the enzyme can affect transcription elongation.<a class="footnote-ref" id="fnref:59" href="#fn:59"><sup>59</sup></a> </p> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/RNA_splicing/a2QEvCRI">RNA splicing</a></li> <li><a href="/facts/MRNA_(guanine-N7-)-methyltransferase/rzseUjy1">mRNA (guanine-N7-)-methyltransferase</a></li> <li><a href="/facts/Post-transcriptional_modification/Hp9Ww9Nk">Post-transcriptional modification</a></li> <li><a href="/facts/Translation_(biology)/JcPC1rth">Translation (biology)</a></li> <li><a href="/facts/Ribosome/CF2u2gtg">Ribosome</a></li> <li><a href="/facts/Transcription_(genetics)/bDgp9HDN">Transcription</a></li> <li><a href="/facts/RNA_Polymerase_II/MK2kgybw">RNA Polymerase II</a></li> <li><a href="/facts/Eukaryotic_transcription/TljvkBjL">Eukaryotic transcription</a></li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Cowling VH (December 2009). "Regulation of mRNA cap methylation". The Biochemical Journal. 425 (2): 295–302. doi:10.1042/BJ20091352. PMC 2825737. PMID 20025612. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825737" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825737</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Mandal SS, Chu C, Wada T, Handa H, Shatkin AJ, Reinberg D (May 2004). "Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II". Proceedings of the National Academy of Sciences of the United States of America. 101 (20): 7572–7. Bibcode:2004PNAS..101.7572M. doi:10.1073/pnas.0401493101. PMC 419647. PMID 15136722. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC419647" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC419647</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Cowling VH (December 2009). "Regulation of mRNA cap methylation". The Biochemical Journal. 425 (2): 295–302. doi:10.1042/BJ20091352. PMC 2825737. PMID 20025612. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825737" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825737</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Fabrega C, Hausmann S, Shen V, Shuman S, Lima CD (January 2004). "Structure and mechanism of mRNA cap (guanine-N7) methyltransferase". Molecular Cell. 13 (1): 77–89. doi:10.1016/s1097-2765(03)00522-7. PMID 14731396. <a href="https://doi.org/10.1016%2Fs1097-2765%2803%2900522-7" target="_blank">https://doi.org/10.1016%2Fs1097-2765%2803%2900522-7</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>Cowling VH (December 2009). "Regulation of mRNA cap methylation". The Biochemical Journal. 425 (2): 295–302. doi:10.1042/BJ20091352. PMC 2825737. PMID 20025612. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825737" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825737</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Fabrega C, Hausmann S, Shen V, Shuman S, Lima CD (January 2004). "Structure and mechanism of mRNA cap (guanine-N7) methyltransferase". Molecular Cell. 13 (1): 77–89. doi:10.1016/s1097-2765(03)00522-7. PMID 14731396. <a href="https://doi.org/10.1016%2Fs1097-2765%2803%2900522-7" target="_blank">https://doi.org/10.1016%2Fs1097-2765%2803%2900522-7</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Ho CK, Sriskanda V, McCracken S, Bentley D, Schwer B, Shuman S (April 1998). "The guanylyltransferase domain of mammalian mRNA capping enzyme binds to the phosphorylated carboxyl-terminal domain of RNA polymerase II". The Journal of Biological Chemistry. 273 (16): 9577–85. doi:10.1074/jbc.273.16.9577. PMID 9545288. <a href="https://doi.org/10.1074%2Fjbc.273.16.9577" target="_blank">https://doi.org/10.1074%2Fjbc.273.16.9577</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>Kim HJ, Jeong SH, Heo JH, Jeong SJ, Kim ST, Youn HD, Han JW, Lee HW, Cho EJ (July 2004). "mRNA capping enzyme activity is coupled to an early transcription elongation". Molecular and Cellular Biology. 24 (14): 6184–93. doi:10.1128/MCB.24.14.6184-6193.2004. PMC 434235. PMID 15226422. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC434235" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC434235</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Watson J (April 8, 2014). Molecular Biology of the Gene. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. pp. 429–455. ISBN 9780321762436. <a href="9780321762436" target="_blank">9780321762436</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>Watson J (April 8, 2014). Molecular Biology of the Gene. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. pp. 429–455. ISBN 9780321762436. <a href="9780321762436" target="_blank">9780321762436</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>Ghosh A, Lima CD (Jul–Aug 2010). "Enzymology of RNA cap synthesis". Wiley Interdisciplinary Reviews: RNA. 1 (1): 152–72. doi:10.1002/wrna.19. PMC 3962952. PMID 21956912. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962952" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962952</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>Cowling VH (December 2009). "Regulation of mRNA cap methylation". The Biochemical Journal. 425 (2): 295–302. doi:10.1042/BJ20091352. PMC 2825737. PMID 20025612. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825737" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825737</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> <li id="fn:13"><p>Ghosh A, Lima CD (Jul–Aug 2010). "Enzymology of RNA cap synthesis". Wiley Interdisciplinary Reviews: RNA. 1 (1): 152–72. doi:10.1002/wrna.19. PMC 3962952. PMID 21956912. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962952" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962952</a> <a href="#fnref:13" class="footnote-back-ref">↩</a></p></li> <li id="fn:14"><p>Wen Y, Yue Z, Shatkin AJ (October 1998). "Mammalian capping enzyme binds RNA and uses protein tyrosine phosphatase mechanism". Proceedings of the National Academy of Sciences of the United States of America. 95 (21): 12226–31. Bibcode:1998PNAS...9512226W. doi:10.1073/pnas.95.21.12226. PMC 22813. PMID 9770468. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC22813" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC22813</a> <a href="#fnref:14" class="footnote-back-ref">↩</a></p></li> <li id="fn:15"><p>Watson J (April 8, 2014). Molecular Biology of the Gene. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. pp. 429–455. ISBN 9780321762436. <a href="9780321762436" target="_blank">9780321762436</a> <a href="#fnref:15" class="footnote-back-ref">↩</a></p></li> <li id="fn:16"><p>Cowling VH (December 2009). "Regulation of mRNA cap methylation". The Biochemical Journal. 425 (2): 295–302. doi:10.1042/BJ20091352. PMC 2825737. PMID 20025612. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825737" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825737</a> <a href="#fnref:16" class="footnote-back-ref">↩</a></p></li> <li id="fn:17"><p>Cowling VH (December 2009). "Regulation of mRNA cap methylation". The Biochemical Journal. 425 (2): 295–302. doi:10.1042/BJ20091352. PMC 2825737. PMID 20025612. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825737" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825737</a> <a href="#fnref:17" class="footnote-back-ref">↩</a></p></li> <li id="fn:18"><p>Ghosh A, Lima CD (Jul–Aug 2010). "Enzymology of RNA cap synthesis". Wiley Interdisciplinary Reviews: RNA. 1 (1): 152–72. doi:10.1002/wrna.19. PMC 3962952. PMID 21956912. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962952" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962952</a> <a href="#fnref:18" class="footnote-back-ref">↩</a></p></li> <li id="fn:19"><p>Shuman S, Schwer B (August 1995). "RNA capping enzyme and DNA ligase: a superfamily of covalent nucleotidyl transferases". Molecular Microbiology. 17 (3): 405–10. doi:10.1111/j.1365-2958.1995.mmi_17030405.x. PMID 8559059. <a href="https://doi.org/10.1111%2Fj.1365-2958.1995.mmi_17030405.x" target="_blank">https://doi.org/10.1111%2Fj.1365-2958.1995.mmi_17030405.x</a> <a href="#fnref:19" class="footnote-back-ref">↩</a></p></li> <li id="fn:20"><p>Gu M, Rajashankar KR, Lima CD (February 2010). "Structure of the Saccharomyces cerevisiae Cet1-Ceg1 mRNA capping apparatus". Structure. 18 (2): 216–27. doi:10.1016/j.str.2009.12.009. PMC 2877398. PMID 20159466. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877398" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877398</a> <a href="#fnref:20" class="footnote-back-ref">↩</a></p></li> <li id="fn:21"><p>Wang SP, Deng L, Ho CK, Shuman S (September 1997). "Phylogeny of mRNA capping enzymes". Proceedings of the National Academy of Sciences of the United States of America. 94 (18): 9573–8. Bibcode:1997PNAS...94.9573W. doi:10.1073/pnas.94.18.9573. PMC 23221. PMID 9275164. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC23221" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC23221</a> <a href="#fnref:21" class="footnote-back-ref">↩</a></p></li> <li id="fn:22"><p>Ghosh A, Lima CD (Jul–Aug 2010). "Enzymology of RNA cap synthesis". Wiley Interdisciplinary Reviews: RNA. 1 (1): 152–72. doi:10.1002/wrna.19. PMC 3962952. PMID 21956912. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962952" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962952</a> <a href="#fnref:22" class="footnote-back-ref">↩</a></p></li> <li id="fn:23"><p>Shuman S, Schwer B (August 1995). "RNA capping enzyme and DNA ligase: a superfamily of covalent nucleotidyl transferases". Molecular Microbiology. 17 (3): 405–10. doi:10.1111/j.1365-2958.1995.mmi_17030405.x. 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