8dcf | pdb_00008dcf
RNA ligase RtcB from Pyrococcus horikoshii in complex with Cu2+ and GTP
Structural highlights
FunctionRTCB_PYRHO tRNA-splicing ligase that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'-phosphodiester. May act as a RNA ligase with broad substrate specificity, and may function toward other RNAs (By similarity). Publication Abstract from PubMedPyrococcus horikoshii (Pho) RtcB exemplifies a family of binuclear transition metal- and GTP-dependent RNA ligases that join 3'-phosphate and 5'-OH ends via RtcB-(histidinyl-N)-GMP and RNA3'pp5'G intermediates. We find that guanylylation of PhoRtcB is optimal with manganese and less effective with cobalt and nickel. Zinc and copper are inactive and potently inhibit manganese-dependent guanylylation. We report crystal structures of PhoRtcB in complexes with GTP and permissive (Mn, Co, Ni) or inhibitory (Zn, Cu) metals. Zinc and copper occupy the M1 and M2 sites adjacent to the GTP phosphates, as do manganese, cobalt, and nickel. The identity/positions of enzymic ligands for M1 (His234, His329, Cys98) and M2 (Cys98, Asp95, His203) are the same for permissive and inhibitory metals. The differences pertain to: (i) the coordination geometries and phosphate contacts of the metals; and (ii) the orientation of the His404 nucleophile with respect to the GTP alpha-phosphate and pyrophosphate leaving group. M2 metal coordination geometry correlates with metal cofactor activity, whereby inhibitory Zn2 and Cu2 assume a tetrahedral configuration and contact only the GTP gamma-phosphate, whereas Mn2, Co2, and Ni2 coordination complexes are pentahedral and contact the beta- and gamma-phosphates. The His404-Nepsilon-Palpha-O(alpha-beta) angle is closer to apical in Mn (179 degrees ), Co (171 degrees ), and Ni (169 degrees ) structures than in Zn (160 degrees ) and Cu (155 degrees ) structures. The octahedral Mn1 geometry in our RtcB*GTP*Mn(2+) structure, in which Mn1 contacts alpha-, beta-, and gamma-phosphates, transitions to a tetrahedral configuration after formation of RtcB*(His404)-GMP*Mn(2+) and departure of pyrophosphate. Structures of RNA ligase RtcB in complexes with divalent cations and GTP.,Jacewicz A, Dantuluri S, Shuman S RNA. 2022 Nov;28(11):1509-1518. doi: 10.1261/rna.079327.122. Epub 2022 Sep 1. PMID:36130078[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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