An Ir(III) Complex Photosensitizer With Strong Visible Light Absorption for Photocatalytic CO2 Reduction

A cyclometalated iridium(III) complex having 2-(pyren-1-yl)-4-methylquinoline ligands [Ir(pyr)] has a strong absorption band in the visible region (ε444nm = 67,000 M−1 cm−1) but does not act as a photosensitizer for photochemical reduction reactions in the presence of triethylamine as an electron donor. Here, 1,3-dimethyl-2-(o-hydroxyphenyl)-2,3-dihydro-1H-benzo[d]imidazole (BI(OH)H) was used instead of the amine, demonstrating that BI(OH)H efficiently quenched the excited state of Ir(pyr) and can undergo the photochemical carbon dioxide (CO2) reduction catalyzed by trans(Cl)-Ru(dmb)(CO)2Cl2 (dmb = 4,4′-dimethyl-2,2′-bipyridine, Ru) to produce formate as the main product. We also synthesized a binuclear complex combining Ir(pyr) and Ruvia an ethylene bridge and investigated its photochemical CO2 reduction activity in the presence of BI(OH)H

Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification

Wybutosine (yW) is a hypermodified nucleoside found in position 37 of tRNAPhe, and is essential for correct phenylalanine codon translation. yW derivatives widely exist in eukaryotes and archaea, and their chemical structures have many species-specific variations. Among them, its hydroxylated derivative, hydroxywybutosine (OHyW), is found in eukaryotes including human, but the modification mechanism remains unknown. Recently, we identified a novel Jumonji C (JmjC)-domain-containing protein, TYW5 (tRNA yW-synthesizing enzyme 5), which forms the OHyW nucleoside by carbon hydroxylation, using Fe(II) ion and 2-oxoglutarate (2-OG) as cofactors. In this work, we present the crystal structures of human TYW5 (hTYW5) in the free and complex forms with 2-OG and Ni(II) ion at 2.5 and 2.8 Å resolutions, respectively. The structure revealed that the catalytic domain consists of a β-jellyroll fold, a hallmark of the JmjC domains and other Fe(II)/2-OG oxygenases. hTYW5 forms a homodimer through C-terminal helix bundle formation, thereby presenting a large, positively charged patch involved in tRNA binding. A comparison with the structures of other JmjC-domain-containing proteins suggested a mechanism for substrate nucleotide recognition. Functional analyses of structure-based mutants revealed the essential Arg residues participating in tRNA recognition by TYW5. These findings extend the repertoire of the tRNA modification enzyme into the Fe(II)/2-OG oxygenase superfamily

Structural basis for translation termination by archaeal RF1 and GTP-bound EF1 complex

ABSTRACT When a stop codon appears at the ribosomal A site, the class I and II release factors (RFs) terminate translation. In eukaryotes and archaea, the class I and II RFs form a heterodimeric complex, and complete the overall translation termination process in a GTP-dependent manner. However, the structural mechanism of the translation termination by the class I and II RF complex remains unresolved. In archaea, archaeal elongation factor 1 alpha (aEF1a), a carrier GTPase for tRNA, acts as a class II RF by forming a heterodimeric complex with archaeal RF1 (aRF1). We report the crystal structure of the aRF1 · aEF1a complex, the first active class I and II RF complex. This structure remarkably resembles the tRNA · EF-Tu complex, suggesting that aRF1 is efficiently delivered to the ribosomal A site, by mimicking tRNA. It provides insights into the mechanism that couples GTP hydrolysis by the class II RF to stop codon recognition and peptidyltRNA hydrolysis by the class I RF. We discuss the different mechanisms by which aEF1a recognizes aRF1 and aPelota, another aRF1-related protein and molecular evolution of the three functions of aEF1a

The Non-Canonical Hydroxylase Structure of YfcM Reveals a Metal Ion-Coordination Motif Required for EF-P Hydroxylation

EF-P is a bacterial tRNA-mimic protein, which accelerates the ribosome-catalyzed polymerization of poly-prolines. In Escherichia coli, EF-P is post-translationally modified on a conserved lysine residue. The post-translational modification is performed in a two-step reaction involving the addition of a β-lysine moiety and the subsequent hydroxylation, catalyzed by PoxA and YfcM, respectively. The β-lysine moiety was previously shown to enhance the rate of poly-proline synthesis, but the role of the hydroxylation is poorly understood. We solved the crystal structure of YfcM and performed functional analyses to determine the hydroxylation mechanism. In addition, YfcM appears to be structurally distinct from any other hydroxylase structures reported so far. The structure of YfcM is similar to that of the ribonuclease YbeY, even though they do not share sequence homology. Furthermore, YfcM has a metal ion-coordinating motif, similar to YbeY. The metal ion-coordinating motif of YfcM resembles a 2-His-1-carboxylate motif, which coordinates an Fe(II) ion and forms the catalytic site of non-heme iron enzymes. Our findings showed that the metal ion-coordinating motif of YfcM plays an essential role in the hydroxylation of the β-lysylated lysine residue of EF-P. Taken together, our results suggested the potential catalytic mechanism of hydroxylation by YfcM

Ruthenium Picolinate Complex as a Redox Photosensitizer With Wide-Band Absorption

Ruthenium(II) picolinate complex, [Ru(dmb)2(pic)]+ (Ru(pic); dmb = 4,4′-dimethyl-2,2′-bipyridine; Hpic = picolinic acid) was newly synthesized as a potential redox photosensitizer with a wider wavelength range of visible-light absorption compared with [Ru(N∧N)3]2+ (N∧N = diimine ligand), which is the most widely used redox photosensitizer. Based on our investigation of its photophysical and electrochemical properties, Ru(pic) was found to display certain advantageous characteristics of wide-band absorption of visible light (λabs < 670 nm) and stronger reduction ability in a one-electron reduced state (E1/2red = −1.86 V vs. Ag/AgNO3), which should function favorably in photon-absorption and electron transfer to the catalyst, respectively. Performing photocatalysis using Ru(pic) as a redox photosensitizer combined with a Re(I) catalyst reduced CO2 to CO under red-light irradiation (λex > 600 nm). TONCO reached 235 and ΦCO was 8.0%. Under these conditions, [Ru(dmb)3]2+ (Ru(dmb)) is not capable of working as a redox photosensitizer because it does not absorb light at λ > 560 nm. Even in irradiation conditions where both Ru(pic) and Ru(dmb) absorb light (λex > 500 nm), using Ru(pic) demonstrated faster CO formation (TOFCO = 6.7 min−1) and larger TONCO (2347) than Ru(dmb) (TOFCO = 3.6 min−1; TONCO = 2100). These results indicate that Ru(pic) is a superior redox photosensitizer over a wider wavelength range of visible-light absorption

Structural and functional insights into IZUMO1 recognition by JUNO in mammalian fertilization

Kato, K., Satouh, Y., Nishimasu, H. et al. Structural and functional insights into IZUMO1 recognition by JUNO in mammalian fertilization. Nat Commun 7, 12198 (2016). https://doi.org/10.1038/ncomms1219

Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA

The CRISPR-associated endonuclease Cas9 can be targeted to specific genomic loci by single guide RNAs (sgRNAs). Here, we report the crystal structure of Streptococcus pyogenes Cas9 in complex with sgRNA and its target DNA at 2.5 Å resolution. The structure revealed a bilobed architecture composed of target recognition and nuclease lobes, accommodating the sgRNA:DNA heteroduplex in a positively charged groove at their interface. Whereas the recognition lobe is essential for binding sgRNA and DNA, the nuclease lobe contains the HNH and RuvC nuclease domains, which are properly positioned for cleavage of the complementary and noncomplementary strands of the target DNA, respectively. The nuclease lobe also contains a carboxyl-terminal domain responsible for the interaction with the protospacer adjacent motif (PAM). This high-resolution structure and accompanying functional analyses have revealed the molecular mechanism of RNA-guided DNA targeting by Cas9, thus paving the way for the rational design of new, versatile genome-editing technologies.National Institutes of Health (U.S.) (Grant 5DP1-MH100706

Crystal structure of Saccharomyces cerevisiae mitochondrial GatFAB reveals a novel subunit assembly in tRNA-dependent amidotransferases

Yeast mitochondrial Gln-mtRNAGln is synthesized by the transamidation of mischarged Glu-mtRNAGln by a non-canonical heterotrimeric tRNA-dependent amidotransferase (AdT). The GatA and GatB subunits of the yeast AdT (GatFAB) are well conserved among bacteria and eukaryota, but the GatF subunit is a fungi-specific ortholog of the GatC subunit found in all other known heterotrimeric AdTs (GatCAB). Here we report the crystal structure of yeast mitochondrial GatFAB at 2.0 Å resolution. The C-terminal region of GatF encircles the GatA-GatB interface in the same manner as GatC, but the N-terminal extension domain (NTD) of GatF forms several additional hydrophobic and hydrophilic interactions with GatA. NTD-deletion mutants displayed growth defects, but retained the ability to respire. Truncation of the NTD in purified mutants reduced glutaminase and transamidase activities when glutamine was used as the ammonia donor, but increased transamidase activity relative to the full-length enzyme when the donor was ammonium chloride. Our structure-based functional analyses suggest the NTD is a trans-acting scaffolding peptide for the GatA glutaminase active site. The positive surface charge and novel fold of the GatF-GatA interface, shown in this first crystal structure of an organellar AdT, stand in contrast with the more conventional, negatively charged bacterial AdTs described previousl

Crystal Structure and Activity of the Endoribonuclease Domain of the piRNA Pathway Factor Maelstrom

SummaryPIWI-interacting RNAs (piRNAs) protect the genome from transposons in animal gonads. Maelstrom (Mael) is an evolutionarily conserved protein, composed of a high-mobility group (HMG) domain and a MAEL domain, and is essential for piRNA-mediated transcriptional transposon silencing in various species, such as Drosophila and mice. However, its structure and biochemical function have remained elusive. Here, we report the crystal structure of the MAEL domain from Drosophila melanogaster Mael, at 1.6 Å resolution. The structure reveals that the MAEL domain has an RNase H-like fold but lacks canonical catalytic residues conserved among RNase H-like superfamily nucleases. Our biochemical analyses reveal that the MAEL domain exhibits single-stranded RNA (ssRNA)-specific endonuclease activity. Our cell-based analyses further indicate that ssRNA cleavage activity appears dispensable for piRNA-mediated transcriptional transposon silencing in Drosophila. Our findings provide clues toward understanding the multiple roles of Mael in the piRNA pathway

Crystal Structure of Staphylococcus aureus Cas9

Summary The RNA-guided DNA endonuclease Cas9 cleaves double-stranded DNA targets with a protospacer adjacent mot if (PAM) and complementarity to the guide RNA. Recently, we harnessed Staphylococcus aureus Cas9 (SaCas9), which is significantly smaller than Streptococcus pyogenes Cas9 (SpCas9), to facilitate efficient in vivo genome editing. Here, we report the crystal structures of SaCas9 in complex with a single guide RNA (sgRNA) and its double-stranded DNA targets, containing the 5′-TTGAAT-3′ PAM and the 5′-TTGGGT-3′ PAM, at 2.6 and 2.7 Å resolutions, respectively. The structures revealed the mechanism of the relaxed recognition of the 5′-NNGRRT-3′ PAM by SaCas9. A structural comparison of SaCas9 with SpCas9 highlighted both structural conservation and divergence, explaining their distinct PAM specificities and orthologous sgRNA recognition. Finally, we applied the structural information about this minimal Cas9 to rationally design compact transcriptional activators and inducible nucleases, to further expand the CRISPR-Cas9 genome editing toolbox.National Institute of General Medical Sciences (U.S.) (Grant T32GM007753)National Institutes of Health (U.S.) (Award 1DP1-MH100706