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| | <StructureSection load='5zyo' size='340' side='right'caption='[[5zyo]], [[Resolution|resolution]] 1.75Å' scene=''> | | <StructureSection load='5zyo' size='340' side='right'caption='[[5zyo]], [[Resolution|resolution]] 1.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5zyo]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZYO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZYO FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5zyo]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZYO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZYO FirstGlance]. <br> |
| - | </td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rlmH, ybeA, b0636, JW0631 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75Å</td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/23S_rRNA_(pseudouridine(1915)-N(3))-methyltransferase 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.177 2.1.1.177] </span></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5zyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zyo OCA], [https://pdbe.org/5zyo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zyo RCSB], [https://www.ebi.ac.uk/pdbsum/5zyo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zyo ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5zyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zyo OCA], [http://pdbe.org/5zyo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zyo RCSB], [http://www.ebi.ac.uk/pdbsum/5zyo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zyo ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RLMH_ECOLI RLMH_ECOLI]] Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA. Specific for fully assembled 70S ribosomes.<ref>PMID:18755835</ref> <ref>PMID:18755836</ref> | + | [https://www.uniprot.org/uniprot/RLMH_ECOLI RLMH_ECOLI] Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA. Specific for fully assembled 70S ribosomes.<ref>PMID:18755835</ref> <ref>PMID:18755836</ref> |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | YbeA from E. coli is a trefoil-knotted SpoU-TrmD (SPOUT) RNA methyltransferase. While its knotted motif plays a key functional role, it is unclear how the knotted topology emerged from evolution. Here, we reverse-engineered an unknotted circular permutant (CP) of YbeA by introducing a new opening at the knotting loop. The resulting CP folded into an unexpected domain-swapped dimer. Untying the knotted loop abrogated its function, perturbed its folding stability and kinetics, and induced allosteric dynamic changes. We speculated that the knotted loop of YbeA is under tension to keep the cofactor in a high-energy configuration while keeping the threading C-terminal helix being knotted. Circular permutation released the mechanical strain thereby allowing the spring-loaded threading helix to flip, to relax, and to form a domain-swapped dimer. Being knotted may be the consequence of selection pressure for the unique structure-function relationship of the SPOUT superfamily that exists in all kingdoms of life.
| + | |
| - | | + | |
| - | Untying a Knotted SPOUT RNA Methyltransferase by Circular Permutation Results in a Domain-Swapped Dimer.,Ko KT, Hu IC, Huang KF, Lyu PC, Hsu SD Structure. 2019 May 14. pii: S0969-2126(19)30126-1. doi:, 10.1016/j.str.2019.04.004. PMID:31104814<ref>PMID:31104814</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 5zyo" style="background-color:#fffaf0;"></div>
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| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Ecoli]] | + | [[Category: Escherichia coli K-12]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Hsu, S T.D]] | + | [[Category: Hsu STD]] |
| - | [[Category: Huang, K F]] | + | [[Category: Huang KF]] |
| - | [[Category: Ko, K T]] | + | [[Category: Ko KT]] |
| - | [[Category: Lyu, P C]] | + | [[Category: Lyu PC]] |
| - | [[Category: Circular permutation]]
| + | |
| - | [[Category: Domain-swapping]]
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| - | [[Category: Knot]]
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| - | [[Category: Methyltransferase]]
| + | |
| - | [[Category: Transferase]]
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