Crystal Structure of the tRNA 3′ Processing Endoribonuclease tRNase Z from Thermotoga maritima

Ishii, Ryohei; Minagawa, Asako; Takaku, Hiroaki; Takagi, Masamichi; Nashimoto, Masayuki; Yokoyama, Shigeyuki

doi:10.1074/jbc.m500355200

Cited by 80 publications

(87 citation statements)

References 41 publications

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“…2C), and the binding site is located at the interface with the β-CASP domain. The binding modes of the two zinc ions in CPSF-73 are similar to those of the two zinc ions in RNase Z [107,108] as well as a bacterial ribonuclease [113]. The structural studies identify a conserved His residue as the general acid, which is activated by a conserved Asp/Glu residue (Fig.…”

Section: Cpsf-73 (Brr5p/ysh1p)mentioning

confidence: 74%

“…Bacterial RNase J1 has 5′-to-3′ exoribonuclease activity on ribosomal RNA precursors [106]. RNase Z, which contains only the metallo-β-lactamase domain (and therefore is not a β-CASP family member), is the ribonuclease essential for the 3′-end processing of tRNA precursors [107,108]. These observations suggest that CPSF-73 could have nuclease activity, and could actually be the endoribonuclease for the cleavage step of pre-mRNA 3′-end processing.…”

Section: Cpsf-73 (Brr5p/ysh1p)mentioning

confidence: 99%

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Protein factors in pre-mRNA 3′-end processing

Mandel

Bai

Tong

2007

Cell. Mol. Life Sci.

355

482

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Most eukaryotic mRNA precursors (pre-mRNAs) must undergo extensive processing, including cleavage and polyadenylation at the 3′-end. Processing at the 3′-end is controlled by sequence elements in the pre-mRNA (cis elements) as well as protein factors. Despite the seeming biochemical simplicity of the processing reactions, more than 14 proteins have been identified for the mammalian complex, and more than 20 proteins have been identified for the yeast complex. The 3′-end processing machinery also has important roles in transcription and splicing. The mammalian machinery contains several sub-complexes, including cleavage and polyadenylation specificity factor (CPSF), cleavage stimulation factor (CstF), cleavage factor I (CF I m ), and cleavage factor II (CF II m ). Additional protein factors include poly(A) polymerase (PAP), poly(A) binding protein (PABP), symplekin, and the C-terminal domain (CTD) of RNA polymerase II largest subunit. The yeast machinery includes cleavage factor IA (CF IA), cleavage factor IB (CF IB), and cleavage and polyadenylation factor (CPF).

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Section: Cpsf-73 (Brr5p/ysh1p)mentioning

confidence: 74%

Section: Cpsf-73 (Brr5p/ysh1p)mentioning

confidence: 99%

Protein factors in pre-mRNA 3′-end processing

Mandel

Bai

Tong

2007

Cell. Mol. Life Sci.

355

482

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“…2b, see below) and RNase Z (Supplemental Fig. 2d) 19,20 , suggesting that they may be unique to RNA/DNA processing nucleases. This feature of the metallo-β-lactamase fold is crucial for the activity of these proteins, as the loop after strand β13 provides one of the ligands (motif C) to the zinc ions in the active site (Supplemental Fig.…”

mentioning

confidence: 99%

Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease

Mandel

Kaneko

Zhang

et al. 2006

Nature

403

524

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Most eukaryotic messenger RNA precursors (pre-mRNAs) undergo extensive maturational processing, including 3'-end cleavage and polyadenylation [1][2][3][4][5][6][7][8] . Despite the characterization of a large number of proteins that are required for the cleavage reaction, the identity of the endoribonuclease is not known 4,9,10 . Recent analyses suggested that the 73 kD subunit of cleavage and polyadenylation specificity factor (CPSF-73) may be the endonuclease for this and related reactions [10][11][12][13][14][15] , although no direct data confirmed this. Here we report the crystal structures of human CPSF-73 at 2.1 Å resolution, complexed with zinc ions and a sulfate that may mimic the phosphate group of the substrate, and the related yeast protein CPSF-100 (Ydh1p) at 2.5 Å resolution. Both CPSF-73 and CPSF-100 contain two domains, a metallo-β-lactamase domain and a novel β-CASP domain. The active site of CPSF-73, with two zinc ions, is located at the interface of the two domains. Purified recombinant CPSF-73 possesses endoribonuclease activity, and mutations that disrupt zinc binding in the active site abolish this activity. Our studies provide the first direct experimental evidence that CPSF-73 is the pre-mRNA 3'-end processing endonuclease. Keywordspolyadenylation; metallo-β-lactamase; pre-mRNA processing; Artemis; V(D)J recombination; double-strand break repair CPSF-73 belongs to the metallo-β-lactamase superfamily of zinc-dependent hydrolases 11,12 . Canonical metallo-β-lactamases contain five signature sequence motifs-Asp (motif 1), His-X-His-X-Asp-His (motif 2), His (motif 3), Asp (motif 4) and His (motif 5), most of which are ligands to the two zinc ions in their active site. Sequence conservation between CPSF-73 and the canonical metallo-β-lactamases is limited to these signature motifs. While the first four motifs can be identified in the N-terminal segment of CPSF-73 (Supplemental Fig. 1a, Supplemental Table 1), the fifth motif was uncertain, with three candidates, A (Asp or Glu), B (His), and C (His) (Supplemental Fig. 1a), in the so-called β-CASP motif 12 . Motif B was proposed to be equivalent to motif 5 in the canonical metallo-β-lactamases. Another subunit of CPSF, CPSF-100, shares sequence conservation (Supplemental Fig. 1b) Fig. 1a) with CPSF-73 but lacks the putative Zn 2+ binding residues.To understand the roles of CPSF-73 and CPSF-100 in pre-mRNA 3'-end processing, we determined the structures of human CPSF-73 (residues 1-460), and yeast CPSF-100 (residues 1-720) (the crystallographic data are summarized in Supplemental Table 2). The two structures obtained for CPSF-73 were crystallized in the absence or presence of 0.5 mM zinc (although both structures contained zinc atoms; see below). We discovered serendipitously that in situ proteolysis by a fungal protease is crucial for the crystallization of yeast CPSF-100 16 .The structure of CPSF-73 can be divided into two domains (Fig. 1a). The N-terminal residues (amino acids 1-208) form a domain similar to the structure of canonical me...

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“…All eukaryotes have a long form (tRNase Z L ), and some have both forms. Recent high resolution crystal structures of bacterial tRNase Z S provide a basis for modeling the active site and binding domains (20,21), but structures of a eukaryotic tRNase Z S , any tRNase Z L , or any tRNase Z-tRNA complex have not yet been reported.The human genome encodes both tRNase Z L and tRNase Z S . tRNase Z L may have arisen from a duplication of the tRNase Z S gene (22), in which the carboxyl region of tRNase Z L retained all the sequence motifs required for catalysis, leaving the amino half free to diverge, perhaps improving the efficiency of pre-tRNA processing or acquiring additional functions.…”

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confidence: 99%

mentioning

confidence: 99%

Naturally Occurring Mutations in Human Mitochondrial Pre-tRNASer(UCN) Can Affect the Transfer Ribonuclease Z Cleavage Site, Processing Kinetics, and Substrate Secondary Structure

Yan¹,

Zareen²,

Levinger

2006

Journal of Biological Chemistry

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tRNAs are transcribed as precursors with a 5 end leader and a 3 end trailer. The 5 end leader is processed by RNase P, and in most organisms in all three kingdoms, transfer ribonuclease (tRNase) Z can endonucleolytically remove the 3 end trailer. Long ( L ) and short ( S ) forms of the tRNase Z gene are present in the human genome. tRNase Z L processes a nuclear-encoded pre-tRNA ϳ1600-fold more efficiently than tRNase Z S and is predicted to have a strong mitochondrial transport signal. tRNase Z L could, thus, process both nuclear-and mitochondrially encoded pre-tRNAs. More than 150 pathogenesis-associated mutations have been found in the mitochondrial genome, most of them in the 22 mitochondrially encoded tRNAs. All the mutations investigated in human mitochondrial tRNA Ser(UCN) affect processing efficiency, and some affect the cleavage site and secondary structure. These changes could affect tRNase Z processing of mutant pre-tRNAs, perhaps contributing to mitochondrial disease.Mitochondria, the intracellular organelles responsible for most of a eukaryotic cell energy production, possess their own maternally inherited genome. The circular 16,568-base pair human mitochondrial genome (1) is bidirectionally transcribed into long polycistronic heavy (H) 4 -and light (L)-strand precursor RNAs. Two rRNAs and 11 mRNAs encoding 13 polypeptides (all of them subunits of complexes in the respiratory transport chain) are punctuated by 22 tRNAs (1 tRNA for each of 18 amino acids and 2 each for leucine and serine with different anticodons) with very little intergenic RNA (2, 3). Several thousand additional polypeptides required for mitochondrial metabolism are nuclear-encoded, cytoplasmically translated and imported.Precursor tRNA transcripts have a 5Ј end leader and a 3Ј end trailer. Eukaryotic nuclear-encoded tRNAs are transcribed from RNA polymerase III promoters with short 5Ј end leaders and 3Ј end trailers ending with a U 3 tail. The characteristic length and sequence of mitochondrial pre-tRNA leaders and trailers, on the other hand, depend on the setting of individual tRNAs among the neighboring functional RNA units (other tRNAs, mRNAs, rRNAs) on the long polycistronic H-and L-strand transcripts (4).The 5Ј end leader is removed from pre-tRNAs by RNase P in a largely conserved, well characterized reaction (5). On the other hand, there are different paths to a mature tRNA 3Ј end (6). In the tRNAs of some prokaryotes, CCA is transcriptionally encoded, and the 3Ј end trailer is removed by the sequential activity of an endonuclease (RNase E) and exonucleases (7,8). In contrast, in most organisms in all three kingdoms and in extranuclear organelles, CCA is not transcriptionally encoded and can be added to the discriminator (the unpaired nucleotide after the 3Ј end of the acceptor stem, which is retained in mature tRNA) after precise endonucleolytic removal of the 3Ј end trailer by tRNase Z (9 -14).Intriguingly, CCA is a tRNase Z anti-determinant that prevents mature tRNA from recycling through tRNase Z, thus ensuring that ...

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Crystal Structure of the tRNA 3′ Processing Endoribonuclease tRNase Z from Thermotoga maritima

Cited by 80 publications

References 41 publications

Protein factors in pre-mRNA 3′-end processing

Protein factors in pre-mRNA 3′-end processing

Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease

Naturally Occurring Mutations in Human Mitochondrial Pre-tRNASer(UCN) Can Affect the Transfer Ribonuclease Z Cleavage Site, Processing Kinetics, and Substrate Secondary Structure

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