4dwq: Difference between revisions
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==RNA ligase RtcB-GMP/Mn(2+) complex== | |||
<StructureSection load='4dwq' size='340' side='right' caption='[[4dwq]], [[Resolution|resolution]] 2.25Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4dwq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/'pyrococcus_shinkaii' 'pyrococcus shinkaii']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4DWQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4DWQ FirstGlance]. <br> | |||
==Function== | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=POP:PYROPHOSPHATE+2-'>POP</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4dwr|4dwr]]</td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rtcB, PH1602 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 'Pyrococcus shinkaii'])</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=4dwq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4dwq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4dwq RCSB], [http://www.ebi.ac.uk/pdbsum/4dwq PDBsum]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[http://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). | [[http://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 == | |||
The RtcB protein has recently been identified as a 3'-phosphate RNA ligase that directly joins an RNA strand ending with a 2',3'-cyclic phosphate to the 5'-hydroxyl group of another RNA strand in a GTP/Mn(2+)-dependent reaction. Here, we report two crystal structures of Pyrococcus horikoshii RNA-splicing ligase RtcB in complex with Mn(2+) alone (RtcB/ Mn(2+)) and together with a covalently bound GMP (RtcB-GMP/Mn(2+)). The RtcB/ Mn(2+) structure (at 1.6 A resolution) shows two Mn(2+) ions at the active site, and an array of sulfate ions nearby that indicate the binding sites of the RNA phosphate backbone. The structure of the RtcB-GMP/Mn(2+) complex (at 2.3 A resolution) reveals the detailed geometry of guanylylation of histidine 404. The critical roles of the key residues involved in the binding of the two Mn(2+) ions, the four sulfates, and GMP are validated in extensive mutagenesis and biochemical experiments, which also provide a thorough characterization for the three steps of the RtcB ligation pathway: (i) guanylylation of the enzyme, (ii) guanylyl-transfer to the RNA substrate, and (iii) overall ligation. These results demonstrate that the enzyme's substrate-induced GTP binding site and the putative reactive RNA ends are in the vicinity of the binuclear Mn(2+) active center, which provides detailed insight into how the enzyme-bound GMP is tansferred to the 3'-phosphate of the RNA substrate for activation and subsequent nucleophilic attack by the 5'-hydroxyl of the second RNA substrate, resulting in the ligated product and release of GMP. | |||
Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3'-terminal phosphate and 5'-OH.,Englert M, Xia S, Okada C, Nakamura A, Tanavde V, Yao M, Eom SH, Konigsberg WH, Soll D, Wang J Proc Natl Acad Sci U S A. 2012 Sep 18;109(38):15235-40. Epub 2012 Sep 4. PMID:22949672<ref>PMID:22949672</ref> | |||
== | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Pyrococcus shinkaii]] | [[Category: Pyrococcus shinkaii]] | ||
[[Category: Englert, M | [[Category: Englert, M]] | ||
[[Category: Okada, C | [[Category: Okada, C]] | ||
[[Category: Soll, D | [[Category: Soll, D]] | ||
[[Category: Wang, J | [[Category: Wang, J]] | ||
[[Category: Xia, S | [[Category: Xia, S]] | ||
[[Category: Yao, M | [[Category: Yao, M]] | ||
[[Category: Guanylylation]] | [[Category: Guanylylation]] | ||
[[Category: Ligase]] | [[Category: Ligase]] | ||
