Structure of the RNA 3′-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer Journal Article
| Authors: | Tanaka, N.; Smith, P.; Shuman, S. |
| Article Title: | Structure of the RNA 3′-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer |
| Abstract: | RNA 3′-phosphate cyclase (RtcA) synthesizes RNA 2′,3′ cyclic phosphate ends via three steps: reaction with ATP to form a covalent RtcA-AMP intermediate; transfer of adenylate to an RNA 3′-phosphate to form RNA(3′)pp(5′)A; and attack of the vicinal O2′ on the 3′-phosphorus to form a 2′,3′ cyclic phosphate. Here we report the 1.7 Å crystal structure of the RtcA-AMP intermediate, which reveals the mechanism of nucleotidyl transfer. Adenylate is linked via a phosphoamide bond to the His309 Ne{open} atom. A network of hydrogen bonds to the ribose O2′ and O3′ accounts for the stringent ribonucleotide preference. Adenine is sandwiched in a hydrophobic pocket between Tyr284 and Pro131 and the preference for adenine is enforced by Phe135, which packs against the purine C2 edge. Two sulfates bound near the adenylate plausibly mimic the 3′-terminal and penultimate phosphates of RNA. The structure illuminates how the four α2/β4 domains contribute to substrate binding and catalysis. © 2010 Elsevier Ltd. |
| Keywords: | controlled study; unclassified drug; nonhuman; protein conformation; protein domain; proteins; molecular dynamics; protein binding; tyrosine; rna; escherichia coli; crystal structure; hydrogen bond; crystallography, x-ray; purines; molecular interaction; catalysis; enzyme structure; enzyme substrate complex; catalytic domain; mutagenesis; molecular conformation; lyase; histidine; amide; ligases; phosphorus; adenine; adenosine phosphate; ribonucleotide; nucleotides; phosphoamide; ribose; rna 3' phosphate cyclase; sulfate; covalent bond; hydrophobicity; nucleotide transport; anions |
| Journal Title: | Structure |
| Volume: | 18 |
| Issue: | 4 |
| ISSN: | 0969-2126 |
| Publisher: | Cell Press |
| Date Published: | 2010-03-01 |
| Start Page: | 449 |
| End Page: | 457 |
| Language: | English |
| DOI: | 10.1016/j.str.2010.01.016 |
| PUBMED: | 20399182 |
| PROVIDER: | scopus |
| PMCID: | PMC2858066 |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 2" - "Export Date: 20 April 2011" - "CODEN: STRUE" - "Source: Scopus" |
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