Structure-guided mutational analysis of T4 RNA ligase 1 Journal Article
| Authors: | Wang, L. K.; Schwer, B.; Shuman, S. |
| Article Title: | Structure-guided mutational analysis of T4 RNA ligase 1 |
| Abstract: | T4 RNA ligase 1 (Rnl1) is a tRNA repair enzyme that circumvents an RNA-damaging host antiviral response. Whereas the three-step reaction scheme of Rnl1 is well established, the structural basis for catalysis has only recently been appreciated as mutational and crystallographic approaches have converged. Here we performed a structure-guided alanine scan of nine conserved residues, including side chains that either contact the ATP substrate via adenine (Leu179, Val230), the 2′-OH (Glu159), or the γ phosphate (Tyr37) or coordinate divalent metal ions at the ATP α phosphate (Glu159, Tyr246) or β phosphate (Asp272, Asp273). We thereby identified Glu159 and Tyr246 as essential for RNA sealing activity in vitro and for tRNA repair in vivo. Structure-activity relationships at Glu159 and Tyr246 were clarified by conservative substitutions. Eliminating the phosphate-binding Tyr37, and the magnesium-binding Asp272 and Asp273 side chains had little impact on sealing activity in vitro or in vivo, signifying that not all atomic interactions in the active site are critical for function. Analysis of mutational effects on individual steps of the ligation pathway underscored how different functional groups come into play during the ligase-adenylylation reaction versus the subsequent steps of RNA-adenylylation and phosphodiester formation. Moreover, the requirements for sealing exogenous preformed RNA-adenylate are more stringent than are those for sealing the RNA-adenylate intermediate formed in situ during ligation of a 5′-PO4 RNA. Published by Cold Spring Harbor Laboratory Press. Copyright © 2006 RNA Society. |
| Keywords: | controlled study; nonhuman; protein conformation; structure activity relation; structure-activity relationship; tyrosine; mutational analysis; amino acid sequence; conserved sequence; molecular sequence data; kinetics; models, molecular; binding sites; dna mutational analysis; alanine; catalysis; adenosine triphosphate; protein structure; transfer rna; rna processing; polydeoxyribonucleotide synthase; glutamic acid; phosphate; aspartic acid; glutamine; rna ligase (atp); phosphate binding protein; viral proteins; adenylyltransferase; adenine; adenylation; magnesium; crystallography; rna repair; rna analysis; adenosine monophosphate; rna ligase; phosphodiesterase; metal ion; polynucleotide ligase; trna breakage; t4 rna ligase 1 |
| Journal Title: | RNA |
| Volume: | 12 |
| Issue: | 12 |
| ISSN: | 1355-8382 |
| Publisher: | Cold Spring Harbor Laboratory Press |
| Date Published: | 2006-12-01 |
| Start Page: | 2126 |
| End Page: | 2134 |
| Language: | English |
| DOI: | 10.1261/rna.271706 |
| PUBMED: | 17068206 |
| PROVIDER: | scopus |
| PMCID: | PMC1664725 |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 6" - "Export Date: 4 June 2012" - "CODEN: RNARF" - "Source: Scopus" |
Altmetric
Citation Impact
BMJ Impact Analytics
Related MSK Work