7lfq
From Proteopedia
(Difference between revisions)
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| - | ==== | + | ==Pyrococcus RNA ligase== |
| - | <StructureSection load='7lfq' size='340' side='right'caption='[[7lfq]]' scene=''> | + | <StructureSection load='7lfq' size='340' side='right'caption='[[7lfq]], [[Resolution|resolution]] 2.70Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7lfq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LFQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LFQ FirstGlance]. <br> |
| - | </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=7lfq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lfq OCA], [https://pdbe.org/7lfq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lfq RCSB], [https://www.ebi.ac.uk/pdbsum/7lfq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lfq ProSAT]</span></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=OCS:CYSTEINESULFONIC+ACID'>OCS</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=7lfq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lfq OCA], [https://pdbe.org/7lfq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lfq RCSB], [https://www.ebi.ac.uk/pdbsum/7lfq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lfq ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/RTCB_PYRHO RTCB_PYRHO] tRNA-splicing ligase that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester. May act as a RNA ligase with broad substrate specificity, and may function toward other RNAs (By similarity). | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | RtcB enzymes comprise a widely distributed family of manganese- and GTP-dependent RNA repair enzymes that join 2',3'-cyclic phosphate ends to 5'-OH ends via RtcB-(histidinyl-N)-GMP, RNA 3'-phosphate, and RNA3'pp5'G intermediates. RtcB can ligate either 5'-OH RNA or 5'-OH DNA strands in vitro. The nucleic acid contacts of RtcB are uncharted. Here we report a 2.7 A crystal structure of Pyrococcus horikoshii RtcB in complex with a 6-mer 5'-OH DNA oligonucleotide (HO)A(1)pT(2)pG(3)pT(4)pC(5)pC(6), which reveals enzymic contacts of Asn202 to the terminal 5'-OH nucleophile; Arg238 to the A(1)pT(2) and T(2)pG(3) phosphates; Arg190 and Gln194 to the T(2)pG(3) phosphate; and an Arg190 pi-cation interaction with the G3 nucleobase. The structural insights affirm functional studies of E. coli RtcB that implicated the conserved counterpart of Arg238 in engagement of the 5'-OH strand for ligation. The essential active site Cys98 that coordinates two manganese ions is oxidized to cysteine sulfonic acid in our structure, raising the prospect that RtcB activity might be sensitive to modulation during oxidative stress. | ||
| + | |||
| + | Structure of 3'-PO(4)/5'-OH RNA ligase RtcB in complex with a 5'-OH oligonucleotide.,Banerjee A, Goldgur Y, Shuman S RNA. 2021 Feb 22;27(5):584-90. doi: 10.1261/rna.078692.121. PMID:33619169<ref>PMID:33619169</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7lfq" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: | + | [[Category: Pyrococcus horikoshii]] |
| + | [[Category: Synthetic construct]] | ||
| + | [[Category: Banerjee A]] | ||
| + | [[Category: Goldgur Y]] | ||
| + | [[Category: Shuman S]] | ||
Revision as of 08:29, 7 December 2022
Pyrococcus RNA ligase
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