Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, <i>Pyrococcus furiosus</i>

Kanai, Akio; Sato, Asako; Fukuda, Yoko; Okada, Kiyoshi; Matsuda, Takashi; Sakamoto, Taiichi; Muto, Y.; Yokoyama, Shigeyuki; Kawai, Gota; Tomita, Masaru

doi:10.1261/rna.1122109

Cited by 17 publications

(31 citation statements)

References 39 publications

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“…The invariance of the H-x-S motif within the USB1 protein family, despite low overall amino acid sequence identity (Figure 2A), supports a critical role in catalysis. The closest structural homologs (DALI server) 24 are the 2Ј, 5Ј RNA ligases from Pyrococcus horikoshii (PDB 1VDX), 25 Pyrococcus furiosus (PDB 2FYH), 26 and Thermus thermophilus (PDB 1IUH), 27 the central domain of the mammalian A-kinase anchoring protein AKAP18␦ (PDB 2VFY), 28 and a 1Ј-2Ј cyclic nucleotide 2Ј phosphodiesterase (CNPase) from Arabidopsis thaliana involved in tRNA splicing (PDB 1FSI). 29 The signature motif residues of rat AKAP18␦ and human USB1 lie in the same position ( Figure 2B).…”

Section: Crystal Structure Of Human Usb1mentioning

confidence: 99%

Aberrant 3′ oligoadenylation of spliceosomal U6 small nuclear RNA in poikiloderma with neutropenia

Hilcenko

Simpson

Finch

et al. 2013

Blood

125

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Key Points• Crystal structure of human USB1 identifies it as a member of the LigT-like superfamily of 2H phosphoesterases.• USB1 protects spliceosomal U6 small nuclear RNA from aberrant 3Ј oligoadenylation.The recessive disorder poikiloderma with neutropenia (PN) is caused by mutations in the C16orf57 gene that encodes the highly conserved USB1 protein.Here, we present the 1.1 Å resolution crystal structure of human USB1, defining it as a member of the LigT-like superfamily of 2H phosphoesterases. We show that human USB1 is a distributive 3-5 exoribonuclease that posttranscriptionally removes uridine and adenosine nucleosides from the 3 end of spliceosomal U6 small nuclear RNA (snRNA), directly catalyzing terminal 2, 3 cyclic phosphate formation. USB1 measures the appropriate length of the U6 oligo(U) tail by reading the position of a key adenine nucleotide (A102) and pausing 5 uridine residues downstream. We show that the 3 ends of U6 snRNA in PN patient lymphoblasts are elongated and unexpectedly carry nontemplated 3 oligo(A) tails that are characteristic of nuclear RNA surveillancetargets. Thus, our study reveals a novel quality control pathway in which posttranscriptional 3-end processing by USB1 protects U6 snRNA from targeting and destruction by the nuclear exosome. Our data implicate aberrant oligoadenylation of U6 snRNA in the pathogenesis of the leukemia predisposition disorder PN. (Blood. 2013;121(6):1028-1038)

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Section: Crystal Structure Of Human Usb1mentioning

confidence: 99%

Aberrant 3′ oligoadenylation of spliceosomal U6 small nuclear RNA in poikiloderma with neutropenia

Hilcenko

Simpson

Finch

et al. 2013

Blood

125

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“…These searches, however, did not reveal any detectable sequence similarity to any other proteins of known structure or function. Using highly sensitive methods for distant homology detection (Ginalski et al 2004) and fold recognition , we mapped Usb1 and hUSB1 to various 2H phosphodiesterase structures, including that of a cyclic nucleotide phosphodiesterase, 1FSI (Hofmann et al 2000), and a 29-59 RNA ligase, 2FYH (Kanai et al 2009). Interestingly, hUSB1 was previously classified as a 2H phosphodiesterase superfamily member (CG16790-like family of eukaryotic ligT ligases) (Mazumder et al 2002).…”

Section: Usb1 Encodes a Putative Phosphodiesterase Whose Potential Camentioning

confidence: 99%

C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3′ end modification

et al. 2012

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C16orf57 encodes a human protein of unknown function, and mutations in the gene occur in poikiloderma with neutropenia (PN), which is a rare, autosomal recessive disease. Interestingly, mutations in C16orf57 were also observed among patients diagnosed with Rothmund-Thomson syndrome (RTS) and dyskeratosis congenita (DC), which are caused by mutations in genes involved in DNA repair and telomere maintenance. A genetic screen in Saccharomyces cerevisiae revealed that the yeast ortholog of C16orf57, USB1 (YLR132C), is essential for U6 small nuclear RNA (snRNA) biogenesis and cell viability. Usb1 depletion destabilized U6 snRNA, leading to splicing defects and cell growth defects, which was suppressed by the presence of multiple copies of the U6 snRNA gene SNR6. Moreover, Usb1 is essential for the generation of a unique feature of U6 snRNA; namely, the 39-terminal phosphate. RNAi experiments in human cells followed by biochemical and functional analyses confirmed that, similar to yeast, C16orf57 encodes a protein involved in the 29,39-cyclic phosphate formation at the 39 end of U6 snRNA. Advanced bioinformatics predicted that C16orf57 encodes a phosphodiesterase whose putative catalytic activity is essential for its function in vivo. Our results predict an unexpected molecular basis for PN, DC, and RTS and provide insight into U6 snRNA 39 end formation.

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“…Also retrieved in the second group was the NMR structure of Pyrococcus furiosus PF0027, a thermophilic enzyme with vigorous 2 ′ ,3 ′ -cyclic phosphodiesterase activity on a tetranucleotide RNA>p substrate yielding an RNA 2 ′ p product, and comparatively weak activity in joining tRNA halves with 2 ′ ,3 ′ -cyclic phosphate and 5 ′ -OH ends (Kanai et al 2009). Two unusual, and somewhat mysterious, features of the strand joining activity of PF0027 (i.e., ones not shared with the E. coli 2H enzyme) include a dependence on GTP and a capacity to join tRNA halves with RNA 2 ′ p and 5 ′ -OH ends (Kanai et al 2009). Mammalian CNPase, for which multiple structures are available (Myllykoski et al 2013), was retrieved in a distinctly lower tier with respect to its homology with ThpR (Z-score 7.3 and 3.5 Å RMSD at 126 positions).…”

Section: Overview Of the Thpr Structurementioning

confidence: 99%

Structure and mechanism of E. coli RNA 2′,3′-cyclic phosphodiesterase

Remus

Jacewicz

Shuman

2014

RNA

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2H (two-histidine) phosphoesterase enzymes are distributed widely in all domains of life and are implicated in diverse RNA and nucleotide transactions, including the transesterification and hydrolysis of cyclic phosphates. Here we report a biochemical and structural characterization of the Escherichia coli 2H protein YadP, which was identified originally as a reversible transesterifying "nuclease/ligase" at RNA 2 ′ ,5 ′ -phosphodiesters. We find that YadP is an "end healing" cyclic phosphodiesterase (CPDase) enzyme that hydrolyzes an HO RNA>p substrate with a 2 ′ ,3 ′ -cyclic phosphodiester to a HO RNAp product with a 2 ′ -phosphomonoester terminus, without concomitant end joining. Thus we rename this enzyme ThpR (two-histidine 2 ′ ,3 ′ -cyclic phosphodiesterase acting on RNA). The 2.0 Å crystal structure of ThpR in a product complex with 2 ′ -AMP highlights the roles of extended histidine-containing motifs 43 ′ leaving group, thereby implicating His43 as a general acid catalyst. His125-Nε coordinates the O1P oxygen of the AMP 2 ′ -phosphate (inferred from geometry to derive from the attacking water nucleophile), pointing to His125 as a general base catalyst. Arg130 makes bidentate contact with the AMP 2 ′ -phosphate, suggesting a role in transition-state stabilization. Consistent with these inferences, changing His43, His125, or Arg130 to alanine effaced the CPDase activity of ThpR. Phe48 makes a π-π stack on the adenine nucleobase. Mutating Phe28 to alanine slowed the CPDase by an order of magnitude. The tertiary structure and extended active site motifs of ThpR are conserved in a subfamily of bacterial and archaeal 2H enzymes.

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Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus

Cited by 17 publications

References 39 publications

Aberrant 3′ oligoadenylation of spliceosomal U6 small nuclear RNA in poikiloderma with neutropenia

Aberrant 3′ oligoadenylation of spliceosomal U6 small nuclear RNA in poikiloderma with neutropenia

C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3′ end modification

Structure and mechanism of E. coli RNA 2′,3′-cyclic phosphodiesterase

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