title: Structure of RNA 3'-phosphate cyclase bound to substrate RNA.
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.
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Kevin K
authors.initials: KK
authors.lastname: Desai
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Craig A
authors.initials: CA
authors.lastname: Bingman
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Chin L
authors.initials: CL
authors.lastname: Cheng
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA BioSciences at Rice and Department of Chemistry, Rice University, Houston, Texas 77005, USA.
authors.forename: George N
authors.initials: GN
authors.lastname: Phillips
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA rtraines@wisc.edu.
authors.forename: Ronald T
authors.initials: RT
authors.lastname: Raines
mesh_terms: D000249:Adenosine Monophosphate / Q000378:metabolism; D002384:Catalysis; D018360:Crystallography, X-Ray; D008025:Ligases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D009154:Mutation / Q000235:genetics; D011485:Protein Binding; D011487:Protein Conformation; D043902:Pyrococcus horikoshii / Q000201:enzymology*; D012313:RNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*
chemical_list: D000249:Adenosine Monophosphate; D012313:RNA; D008025:Ligases; C037451:RNA 3'-terminal phosphate cyclase
keywords: 2′,3′-cyclic phosphate termini; RNA 3′-phosphate termini; RtcA