Structures of RNA 3′-phosphate cyclase bound to ATP reveal the mechanism of nucleotidyl transfer and metal-assisted catalysis Journal Article
| Authors: | Chakravarty, A. K.; Smith, P.; Shuman, S. |
| Article Title: | Structures of RNA 3′-phosphate cyclase bound to ATP reveal the mechanism of nucleotidyl transfer and metal-assisted catalysis |
| Abstract: | RNA 3′-phosphate cyclase (RtcA) synthesizes RNA 2′,3′ cyclic phosphate ends via three steps: reaction with ATP to form a covalent RtcA-(histidinyl-Nε)-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 and release AMP. Here we report the crystal structures of RtcA·ATP, RtcA·ATP·Mn 2+, and RtcA·ATP·Co 2+ substrate complexes and an RtcA·AMP product complex. Together with the structures of RtcA apoenzyme and the covalent RtcA-AMP intermediate, they illuminate the mechanism of nucleotidyl transfer, especially the stereochemical transitions at the AMP phosphate, the critical role of the metal in orienting the PP i leaving group of ATP during step 1, and the protein conformational switches that accompany substrate binding and product release. The octahedral metal complex of RtcA·ATP·Mn 2+ includes nonbridging oxygens from each of the ATP phosphates, two waters, and Glu14 as the sole RtcA component. Whereas the RtcA adenylylation step is metal-catalyzed, the subsequent steps in the cyclization pathway are metal-independent. |
| Keywords: | unclassified drug; protein conformation; oxygen; protein; protein binding; escherichia coli; crystal structure; models, molecular; catalysis; adenosine triphosphate; cobalt; protein structure; cyclization; crystallization; enzyme release; phosphate; stereochemistry; ligases; covalent catalysis; adenosine phosphate; adenylation; x-ray diffraction; manganese; rna 3' phosphate cyclase; rna modification; glu14 protein; oligonucleotide probes; rna nucleotidyltransferases |
| Journal Title: | Proceedings of the National Academy of Sciences of the United States of America |
| Volume: | 108 |
| Issue: | 52 |
| ISSN: | 0027-8424 |
| Publisher: | National Academy of Sciences |
| Date Published: | 2011-12-27 |
| Start Page: | 21034 |
| End Page: | 21039 |
| Language: | English |
| DOI: | 10.1073/pnas.1115560108 |
| PROVIDER: | scopus |
| PMCID: | PMC3248511 |
| PUBMED: | 22167800 |
| DOI/URL: | |
| Notes: | --- - "Export Date: 1 March 2012" - "CODEN: PNASA" - "Source: Scopus" |
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