4O89

Crystal structure of RtcA, the RNA 3'-terminal phosphate cyclase from Pyrococcus horikoshii.

Summary for 4O89

• Entry DOI: 10.2210/pdb4o89/pdb
• Related: 4O8J
• Descriptor: RNA 3'-terminal phosphate cyclase, CITRIC ACID (3 entities in total)
• Functional Keywords: rna 3'-cyclase, ligase
• Biological source: Pyrococcus horikoshii
• Total number of polymer chains: 2
• Total formula weight: 74826.42

Authors

Desai, K.K.,Bingman, C.A.,Phillips Jr., G.N.,Raines, R.T. (deposition date: 2013-12-26, release date: 2014-09-10, Last modification date: 2024-02-28)

Primary citation

Desai, K.K.,Bingman, C.A.,Cheng, C.L.,Phillips Jr., G.N.,Raines, R.T.
Structure of RNA 3'-phosphate cyclase bound to substrate RNA.
Rna, 20:1560-1566, 2014

PubMed Abstract: RNA 3'-phosphate cyclase (RtcA) catalyzes the ATP-dependent cyclization of a 3'-phosphate to form a 2',3'-cyclic phosphate at RNA termini. Cyclization proceeds through RtcA-AMP and RNA(3')pp(5')A covalent intermediates, which are analogous to intermediates formed during catalysis by the tRNA ligase RtcB. Here we present a crystal structure of Pyrococcus horikoshii RtcA in complex with a 3'-phosphate terminated RNA and adenosine in the AMP-binding pocket. Our data reveal that RtcA recognizes substrate RNA by ensuring that the terminal 3'-phosphate makes a large contribution to RNA binding. Furthermore, the RNA 3'-phosphate is poised for in-line attack on the P-N bond that links the phosphorous atom of AMP to N(ε) of His307. Thus, we provide the first insights into RNA 3'-phosphate termini recognition and the mechanism of 3'-phosphate activation by an Rtc enzyme.

PubMed: 25161314
DOI: 10.1261/rna.045823.114

Experimental method

X-RAY DIFFRACTION (1.9 Å)