| Literature DB >> 31499460 |
Ananthanarayanan Kumar1, Marcello Clerici2, Lena M Muckenfuss2, Lori A Passmore3, Martin Jinek4.
Abstract
The polyadenosine (Entities:
Mesh:
Substances:
Year: 2019 PMID: 31499460 PMCID: PMC6900580 DOI: 10.1016/j.sbi.2019.08.001
Source DB: PubMed Journal: Curr Opin Struct Biol ISSN: 0959-440X Impact factor: 6.809
Figure 1Polyadenylation signals and RNA recognition sites of the 3′-end processing machinery in yeast and human pre-mRNAs.
Protein complexes that are proposed to recognize specific cis-acting elements within the polyadenylation signal are listed below their consensus sequences. Arrows indicate cleavage positions.
Yeast and human mRNA 3′-end processing machinery
| Yeast complex | Module | Yeast protein | M.W. (kDa) | Human Protein | M.W. | Human complex | % Sequence identity (similarity) | Proposed role |
|---|---|---|---|---|---|---|---|---|
| CPF | Polymerase | 65 | 83 | 40 (59) | ||||
| Cft1/Yhh1 | 153 | CPSF160/CPSF1 | 161 | CPSF | 17 (34) | Scaffold | ||
| Pfs2 | 53 | WDR33 | 146 | 37 (57) | Scaffold, RNA binding | |||
| Fip1 | 36 | hFip1 | 67 | 22 (34) | Binds Pap1 | |||
| Yth1 | 25 | CPSF30/CPSF4 | 30 | 36 (51) | RNA binding | |||
| Nuclease | Cft2/Ydh1 | 96 | CPSF100/CPSF2 | 88 | 22 (41) | (Pseudo-)endonuclease | ||
| 88 | 77 | 44 (65) | ||||||
| Mpe1 | 50 | RBBP6 | 202 | 28 (48) | RNA binding | |||
| Phosphatase | Pta1 | 89 | Symplekin | 141 | 17 (37) | Scaffold | ||
| Ref2 | 60 | n.d. | – | – | Regulates Glc7 | |||
| Pti1 | 47 | n.d. | – | – | Scaffold | |||
| Swd2/Cps35 | 37 | WDR82 | 35 | 34 (52) | Transcription termination | |||
| 36 | 38 | 85 (93) | ||||||
| 24 | 23 | 44 (65) | ||||||
| CF IA | Rna14 | 78 | CstF77/CSTF3 | 83 | CstF | 26 (42) | Stoichiometry of 2, scaffold | |
| Rna15 | 33 | CstF64/CSTF2 | 61 | 27 (41) | Stoichiometry of 2, RNA binding | |||
| n.d. | CstF50/CSTF1 | 48 | – | |||||
| Clp1 | 50 | hClp1 | 48 | CF IIm | 27 (44) | RNA kinase in human | ||
| Pcf11 | 72 | hPcf11 | 173 | 21 (32) | Binds Pol II | |||
| CF IB | Hrp1 | 60 | n.d. | – | – | RNA binding | ||
| n.d. | CFIm25/CPSF5/NUDT21 | 26 | CF Im | – | RNA binding | |||
| n.d. | CFIm68/CPSF6 | 59 | – | RNA binding | ||||
| n.d. | CFIm59/CPSF7 | 52 | – | RNA binding |
n.d., none detected.
Enzymes in bold.
Yeast polymerase and nuclease modules comprise the ‘Core CPF’ (CPFcore).
Figure 2Molecular architecture of the structural scaffolds of yeast CPF/human CPSF and mechanism of polyadenylation signal recognition.
(a) Structure of the yeast Cft1–Pfs2–Yth1 complex (PDB code 6EOJ). (b) Structure of the human CPSF160–WDR33–CPSF30 complex bound to AAUAAA PAS RNA (PDB code 6FUW). Protein regions not observed or present in the shown structures are indicated in grey in the domain architecture diagrams above each structure. (c) Specific recognition of the Hoogsteen base pair formed by U3 and A6 of the AAUAAA PAS by a hydrophobic cavity formed by the N-terminal extension of WDR33. (d) Molecular details of AA dinucleotide recognition by CPSF30 zinc finger (ZF) domains 2 (left panel) and 3 (right panel). Hydrogen-bonding interactions are depicted with dashed lines.
Figure 3Structures of the Ysh1/CPSF73 endonuclease and model for 3′-end processing.
(a) X-ray crystal structure of human CPSF73 showing the β-CASP and metallo-β-lactamase (MβL) domains (PDB code 2I7T). Zinc ions are shown as grey spheres and their coordination is indicated with dashed lines. In the active site, a hydroxide ion (shown as a blue sphere) is the attacking nucleophile and a sulfate molecule mimics the phosphate group of an RNA substrate. (b) Crystal structure of Ysh1 bound to ubiquitin-like domain (UBL) of Mpe1 (PDB code 6I1D). Inset shows superposition with the CPSF73 structure, revealing movement of two helices that could resemble a pre-activation state where the nuclease is primed for activation. Ysh1 is shown in gold, Mpe1 in orange and CPSF73 in pink. The active site tunnel lies behind the two helices formed by residues 95 to 111 (helix 1) and 122 to 136 (helix 2) of Ysh1 as indicated. (c) A model of mRNA 3′-end processing. The polymerase module hub of Cft1/CPSF160, Pfs2/WDR33 and Yth1/CPSF30 is shown with other subunits and factors surrounding it. Accessory cleavage factors are CF IA, CF IB, CstF, CF Im and CF IIm. RNA is colored as in Figure 1. Questions remaining are indicated.