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Structural characterization of the principal mRNA-export factor Mex67-Mtr2 from Chaetomium thermophilum.

Aibara S, Valkov E, Lamers MH, Dimitrova L, Hurt E, Stewart M - Acta Crystallogr F Struct Biol Commun (2015)

Bottom Line: Members of the Mex67-Mtr2/NXF-NXT1 family are the principal mediators of the nuclear export of mRNA.Mex67/NXF1 has a modular structure based on four domains (RRM, LRR, NTF2-like and UBA) that are thought to be present across species, although the level of sequence conservation between organisms, especially in lower eukaryotes, is low.Moreover, the resolution of crystal structures obtained with the C. thermophilum domains was often higher than that obtained previously and, when combined with solution and biochemical studies, provided insight into the structural organization, self-association and RNA-binding properties of Mex67-Mtr2 that facilitate mRNA nuclear export.

View Article: PubMed Central - HTML - PubMed

Affiliation: MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England.

ABSTRACT
Members of the Mex67-Mtr2/NXF-NXT1 family are the principal mediators of the nuclear export of mRNA. Mex67/NXF1 has a modular structure based on four domains (RRM, LRR, NTF2-like and UBA) that are thought to be present across species, although the level of sequence conservation between organisms, especially in lower eukaryotes, is low. Here, the crystal structures of these domains from the thermophilic fungus Chaetomium thermophilum are presented together with small-angle X-ray scattering (SAXS) and in vitro RNA-binding data that indicate that, not withstanding the limited sequence conservation between different NXF family members, the molecules retain similar structural and RNA-binding properties. Moreover, the resolution of crystal structures obtained with the C. thermophilum domains was often higher than that obtained previously and, when combined with solution and biochemical studies, provided insight into the structural organization, self-association and RNA-binding properties of Mex67-Mtr2 that facilitate mRNA nuclear export.

No MeSH data available.


(a) Overview of the 2.4 Å resolution crystal structure of ctMex67RRM. (b) A schematic illustration of the secondary-structural elements present in the RRM domain, which showed the characteristic βαββαβ fold. The RRM domain from ctMex67 had a short β-strand prior to β4 that was not found in other organisms (denoted β4′). (c) Three representative views of the final 2Fo − Fc maps for the ctMex67RRM structure contoured at the 1σ level. (d) Overview of the 1.7 Å resolution crystal structure of ctMex67LRR. (e) Schematic illustration of the secondary-structural elements present in the LRR domain whereby tandem repeating α-helices and β-sheets generate a curved structure. Disordered regions are shown as red dotted lines. The LRR domain from ctMex67 includes an extra helix insertion between α2b and β2 when compared with the H. sapiens homologue. (f) Three representative views of the final 2Fo − Fc maps for the ctMex67LRR structure contoured at the 1σ level.
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fig2: (a) Overview of the 2.4 Å resolution crystal structure of ctMex67RRM. (b) A schematic illustration of the secondary-structural elements present in the RRM domain, which showed the characteristic βαββαβ fold. The RRM domain from ctMex67 had a short β-strand prior to β4 that was not found in other organisms (denoted β4′). (c) Three representative views of the final 2Fo − Fc maps for the ctMex67RRM structure contoured at the 1σ level. (d) Overview of the 1.7 Å resolution crystal structure of ctMex67LRR. (e) Schematic illustration of the secondary-structural elements present in the LRR domain whereby tandem repeating α-helices and β-sheets generate a curved structure. Disordered regions are shown as red dotted lines. The LRR domain from ctMex67 includes an extra helix insertion between α2b and β2 when compared with the H. sapiens homologue. (f) Three representative views of the final 2Fo − Fc maps for the ctMex67LRR structure contoured at the 1σ level.

Mentions: The 2.4 Å resolution crystal structure of ctMex67RRM resembled that of hsNXF1RRM (Liker et al., 2000 ▸; Teplova et al., 2011 ▸; PDB entries 1fo1 and 3rw6) and was based on the characteristic RRM βαββαβ fold (Figs. 2 ▸a, 2 ▸b and 2 ▸c). Like other NXF family members, ctMex67RRM did not contain a typical RRM consensus sequence that is based on two motifs: RNP1, (K/R)o-G-(F/Y)o-(G/A)i-Fo-Vi-Xo-(F/Y)i, and RNP2, (L/I)i-(Y/F)o-(V/I)i-(G/N)o-(G/N)o-(L/M)i, where the subscript ‘o’ or ‘i’ signifies whether the side chain is surface-exposed or facing the core of the RRM fold (Liker et al., 2000 ▸; Maris et al., 2005 ▸). In ctMex67RRM the RNP1 (residues 143–150) and RNP2 (residues 101–106) sequences were G-Do-Yo-Vi-Wo-Li-Ko-Vi and Ii-Ko-Ii-Lo-G-Li, respectively. The RNP2 motif appeared to be more conserved than RNP1, although the characteristic aromatic group at position 2 that typically forms ring-stacking interactions with RNA was instead lysine in ctMex67RRM. The large deviations from the RNP1 and RNP2 sequences found in different members of the NXF1/Mex67 family may reflect that they bind RNA in a more general, non-base-specific way, as appeared to be the case in the crystal structure of hsNXF1RRM-LRR–CTE-B, in which the hsNXF1 RRM domain formed mainly phosphate–backbone interactions with the CTE-B RNA (Teplova et al., 2011 ▸). The 1.7 Å resolution crystal structure of ctMex67LRR showed the characteristic pattern of alternating α-helices and β-strands arranged to form a gently curving structure similar to that seen in this domain in homologous structures (Figs. 2 ▸d, 2 ▸e and 2 ▸f; Liker et al., 2000 ▸; Teplova et al., 2011 ▸), although ctMex67LRR had an additional α-helix inserted between the first α-helix and β-strand of the domain core (Fig. 2 ▸e; denoted α2c).


Structural characterization of the principal mRNA-export factor Mex67-Mtr2 from Chaetomium thermophilum.

Aibara S, Valkov E, Lamers MH, Dimitrova L, Hurt E, Stewart M - Acta Crystallogr F Struct Biol Commun (2015)

(a) Overview of the 2.4 Å resolution crystal structure of ctMex67RRM. (b) A schematic illustration of the secondary-structural elements present in the RRM domain, which showed the characteristic βαββαβ fold. The RRM domain from ctMex67 had a short β-strand prior to β4 that was not found in other organisms (denoted β4′). (c) Three representative views of the final 2Fo − Fc maps for the ctMex67RRM structure contoured at the 1σ level. (d) Overview of the 1.7 Å resolution crystal structure of ctMex67LRR. (e) Schematic illustration of the secondary-structural elements present in the LRR domain whereby tandem repeating α-helices and β-sheets generate a curved structure. Disordered regions are shown as red dotted lines. The LRR domain from ctMex67 includes an extra helix insertion between α2b and β2 when compared with the H. sapiens homologue. (f) Three representative views of the final 2Fo − Fc maps for the ctMex67LRR structure contoured at the 1σ level.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4498709&req=5

fig2: (a) Overview of the 2.4 Å resolution crystal structure of ctMex67RRM. (b) A schematic illustration of the secondary-structural elements present in the RRM domain, which showed the characteristic βαββαβ fold. The RRM domain from ctMex67 had a short β-strand prior to β4 that was not found in other organisms (denoted β4′). (c) Three representative views of the final 2Fo − Fc maps for the ctMex67RRM structure contoured at the 1σ level. (d) Overview of the 1.7 Å resolution crystal structure of ctMex67LRR. (e) Schematic illustration of the secondary-structural elements present in the LRR domain whereby tandem repeating α-helices and β-sheets generate a curved structure. Disordered regions are shown as red dotted lines. The LRR domain from ctMex67 includes an extra helix insertion between α2b and β2 when compared with the H. sapiens homologue. (f) Three representative views of the final 2Fo − Fc maps for the ctMex67LRR structure contoured at the 1σ level.
Mentions: The 2.4 Å resolution crystal structure of ctMex67RRM resembled that of hsNXF1RRM (Liker et al., 2000 ▸; Teplova et al., 2011 ▸; PDB entries 1fo1 and 3rw6) and was based on the characteristic RRM βαββαβ fold (Figs. 2 ▸a, 2 ▸b and 2 ▸c). Like other NXF family members, ctMex67RRM did not contain a typical RRM consensus sequence that is based on two motifs: RNP1, (K/R)o-G-(F/Y)o-(G/A)i-Fo-Vi-Xo-(F/Y)i, and RNP2, (L/I)i-(Y/F)o-(V/I)i-(G/N)o-(G/N)o-(L/M)i, where the subscript ‘o’ or ‘i’ signifies whether the side chain is surface-exposed or facing the core of the RRM fold (Liker et al., 2000 ▸; Maris et al., 2005 ▸). In ctMex67RRM the RNP1 (residues 143–150) and RNP2 (residues 101–106) sequences were G-Do-Yo-Vi-Wo-Li-Ko-Vi and Ii-Ko-Ii-Lo-G-Li, respectively. The RNP2 motif appeared to be more conserved than RNP1, although the characteristic aromatic group at position 2 that typically forms ring-stacking interactions with RNA was instead lysine in ctMex67RRM. The large deviations from the RNP1 and RNP2 sequences found in different members of the NXF1/Mex67 family may reflect that they bind RNA in a more general, non-base-specific way, as appeared to be the case in the crystal structure of hsNXF1RRM-LRR–CTE-B, in which the hsNXF1 RRM domain formed mainly phosphate–backbone interactions with the CTE-B RNA (Teplova et al., 2011 ▸). The 1.7 Å resolution crystal structure of ctMex67LRR showed the characteristic pattern of alternating α-helices and β-strands arranged to form a gently curving structure similar to that seen in this domain in homologous structures (Figs. 2 ▸d, 2 ▸e and 2 ▸f; Liker et al., 2000 ▸; Teplova et al., 2011 ▸), although ctMex67LRR had an additional α-helix inserted between the first α-helix and β-strand of the domain core (Fig. 2 ▸e; denoted α2c).

Bottom Line: Members of the Mex67-Mtr2/NXF-NXT1 family are the principal mediators of the nuclear export of mRNA.Mex67/NXF1 has a modular structure based on four domains (RRM, LRR, NTF2-like and UBA) that are thought to be present across species, although the level of sequence conservation between organisms, especially in lower eukaryotes, is low.Moreover, the resolution of crystal structures obtained with the C. thermophilum domains was often higher than that obtained previously and, when combined with solution and biochemical studies, provided insight into the structural organization, self-association and RNA-binding properties of Mex67-Mtr2 that facilitate mRNA nuclear export.

View Article: PubMed Central - HTML - PubMed

Affiliation: MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England.

ABSTRACT
Members of the Mex67-Mtr2/NXF-NXT1 family are the principal mediators of the nuclear export of mRNA. Mex67/NXF1 has a modular structure based on four domains (RRM, LRR, NTF2-like and UBA) that are thought to be present across species, although the level of sequence conservation between organisms, especially in lower eukaryotes, is low. Here, the crystal structures of these domains from the thermophilic fungus Chaetomium thermophilum are presented together with small-angle X-ray scattering (SAXS) and in vitro RNA-binding data that indicate that, not withstanding the limited sequence conservation between different NXF family members, the molecules retain similar structural and RNA-binding properties. Moreover, the resolution of crystal structures obtained with the C. thermophilum domains was often higher than that obtained previously and, when combined with solution and biochemical studies, provided insight into the structural organization, self-association and RNA-binding properties of Mex67-Mtr2 that facilitate mRNA nuclear export.

No MeSH data available.