3TUT

Crystal structure of RtcA.ATP binary complex

Summary for 3TUT

• Entry DOI: 10.2210/pdb3tut/pdb
• Related: 1QMH 1QMI 3KGD 3TUX 3TV1 3TW3
• Descriptor: RNA 3'-terminal phosphate cyclase, ADENOSINE-5'-TRIPHOSPHATE, SULFATE ION, ... (6 entities in total)
• Functional Keywords: cyclase family, cyclization of rna 3'-phosphate ends, transferase
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P46849
• Total number of polymer chains: 1
• Total formula weight: 39061.93

Authors

Chakravarty, A.K.,Smith, P.,Shuman, S. (deposition date: 2011-09-18, release date: 2011-12-28, Last modification date: 2023-09-13)

Primary citation

Chakravarty, A.K.,Smith, P.,Shuman, S.
Structures of RNA 3'-phosphate cyclase bound to ATP reveal the mechanism of nucleotidyl transfer and metal-assisted catalysis.
Proc.Natl.Acad.Sci.USA, 108:21034-21039, 2011

PubMed 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.

PubMed: 22167800
DOI: 10.1073/pnas.1115560108

Experimental method

X-RAY DIFFRACTION (1.58 Å)