6vt0: Difference between revisions
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<StructureSection load='6vt0' size='340' side='right'caption='[[6vt0]], [[Resolution|resolution]] 2.00Å' scene=''> | <StructureSection load='6vt0' size='340' side='right'caption='[[6vt0]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6vt0]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VT0 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[6vt0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Naegleria_gruberi Naegleria gruberi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VT0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VT0 FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.002Å</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=6vt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vt0 OCA], [https://pdbe.org/6vt0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vt0 RCSB], [https://www.ebi.ac.uk/pdbsum/6vt0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vt0 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/D2W2Z5_NAEGR D2W2Z5_NAEGR] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Naegleria gruberi RNA ligase (NgrRnl) exemplifies the Rnl5 family of adenosine triphosphate (ATP)-dependent polynucleotide ligases that seal 3'-OH RNA strands in the context of 3'-OH/5'-PO4 nicked duplexes. Like all classic ligases, NgrRnl forms a covalent lysyl-AMP intermediate. A two-metal mechanism of lysine adenylylation was established via a crystal structure of the NgrRnl*ATP*(Mn2+)2 Michaelis complex. Here we conducted an alanine scan of active site constituents that engage the ATP phosphates and the metal cofactors. We then determined crystal structures of ligase-defective NgrRnl-Ala mutants in complexes with ATP/Mn2+. The unexpected findings were that mutations K170A, E227A, K326A and R149A (none of which impacted overall enzyme structure) triggered adverse secondary changes in the active site entailing dislocations of the ATP phosphates, altered contacts to ATP, and variations in the numbers and positions of the metal ions that perverted the active sites into off-pathway states incompatible with lysine adenylylation. Each alanine mutation elicited a distinctive off-pathway distortion of the ligase active site. Our results illuminate a surprising plasticity of the ligase active site in its interactions with ATP and metals. More broadly, they underscore a valuable caveat when interpreting mutational data in the course of enzyme structure-function studies. | |||
Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation.,Unciuleac MC, Goldgur Y, Shuman S Nucleic Acids Res. 2020 Apr 21. pii: 5823197. doi: 10.1093/nar/gkaa238. PMID:32315072<ref>PMID:32315072</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6vt0" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[RNA ligase|RNA ligase]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Naegleria gruberi]] | ||
[[Category: | [[Category: Goldgur Y]] | ||
[[Category: | [[Category: Shuman S]] | ||
[[Category: | [[Category: Unciuleac MC]] | ||
Latest revision as of 11:19, 11 October 2023
Naegleria gruberi RNA ligase K170A mutant apoNaegleria gruberi RNA ligase K170A mutant apo
Structural highlights
FunctionPublication Abstract from PubMedNaegleria gruberi RNA ligase (NgrRnl) exemplifies the Rnl5 family of adenosine triphosphate (ATP)-dependent polynucleotide ligases that seal 3'-OH RNA strands in the context of 3'-OH/5'-PO4 nicked duplexes. Like all classic ligases, NgrRnl forms a covalent lysyl-AMP intermediate. A two-metal mechanism of lysine adenylylation was established via a crystal structure of the NgrRnl*ATP*(Mn2+)2 Michaelis complex. Here we conducted an alanine scan of active site constituents that engage the ATP phosphates and the metal cofactors. We then determined crystal structures of ligase-defective NgrRnl-Ala mutants in complexes with ATP/Mn2+. The unexpected findings were that mutations K170A, E227A, K326A and R149A (none of which impacted overall enzyme structure) triggered adverse secondary changes in the active site entailing dislocations of the ATP phosphates, altered contacts to ATP, and variations in the numbers and positions of the metal ions that perverted the active sites into off-pathway states incompatible with lysine adenylylation. Each alanine mutation elicited a distinctive off-pathway distortion of the ligase active site. Our results illuminate a surprising plasticity of the ligase active site in its interactions with ATP and metals. More broadly, they underscore a valuable caveat when interpreting mutational data in the course of enzyme structure-function studies. Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation.,Unciuleac MC, Goldgur Y, Shuman S Nucleic Acids Res. 2020 Apr 21. pii: 5823197. doi: 10.1093/nar/gkaa238. PMID:32315072[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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