4IT0

Structure of the RNA ligase RtcB-GMP/Mn(II) complex

Summary for 4IT0

• Entry DOI: 10.2210/pdb4it0/pdb
• Related: 4ISZ 4iSJ
• Related PRD ID: PRD_900003
• Descriptor: tRNA-splicing ligase RtcB, beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose, MANGANESE (II) ION, ... (6 entities in total)
• Functional Keywords: rna ligase, ligase
• Biological source: Pyrococcus horikoshii; More
• Total number of polymer chains: 2
• Total formula weight: 110257.60

Authors

Desai, K.K.,Bingman, C.A.,Phillips Jr., G.N.,Raines, R.T. (deposition date: 2013-01-17, release date: 2013-03-20, Last modification date: 2024-02-28)

Primary citation

Desai, K.K.,Bingman, C.A.,Phillips, G.N.,Raines, R.T.
Structures of the Noncanonical RNA Ligase RtcB Reveal the Mechanism of Histidine Guanylylation.
Biochemistry, 52:2518-2525, 2013

PubMed Abstract: RtcB is an atypical RNA ligase that joins either 2',3'-cyclic phosphate or 3'-phosphate termini to 5'-hydroxyl termini. In contrast to typical RNA ligases, which rely on ATP and Mg(II), catalysis by RtcB is dependent on GTP and Mn(II) with ligation proceeding through a covalent RtcB-histidine-GMP intermediate. Here, we present three structures of Pyrococcus horikoshii RtcB complexes that capture snapshots along the entire guanylylation pathway. These structures show that prior to binding GTP, a single manganese ion (Mn1) is bound to RtcB. To capture the step immediately preceding RtcB guanylylation, we determined a structure of RtcB in complex with Mn(II) and the unreactive GTP analogue guanosine 5'-(α-thio)triphosphate (GTPαS). This structure shows that Mn1 is poised to stabilize the pentavalent transition state of guanylylation while a second manganese ion (Mn2) is coordinated to a nonbridging oxygen of the γ-phosphoryl group. The pyrophosphate leaving group of GTPαS is oriented apically to His404 with the ε-nitrogen poised for in-line attack on the α-phosphorus atom. The structure of RtcB in complex with GTPαS also reveals the network of hydrogen bonds that recognize GTP and illuminates the significant conformational changes that accompany the binding of this cofactor. Finally, a structure of the enzymic histidine-GMP intermediate depicts the end of the guanylylation pathway. The ensuing molecular description of the RtcB guanylylation pathway shows that RtcB and classical ATP- and Mg(II)-dependent nucleic acid ligases have converged upon a similar two-metal mechanism for formation of the nucleotidylated enzyme intermediate.

PubMed: 23560983
DOI: 10.1021/bi4002375

Experimental method

X-RAY DIFFRACTION (2.4 Å)