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Structural insights into TDP-43 in nucleic-acid binding and domain interactions.

Kuo PH, Doudeva LG, Wang YT, Shen CK, Yuan HS - Nucleic Acids Res. (2009)

Bottom Line: The crystal structure reveals the basis of TDP-43's TG/UG preference in nucleic acids binding.It also reveals that RRM2 domain has an atypical RRM-fold with an additional beta-strand involved in making protein-protein interactions.These studies thus characterize the recognition between TDP-43 and nucleic acids and the mode of RRM2 self association, and provide molecular models for understanding the role of TDP-43 in cystic fibrosis and the neurodegenerative diseases related to TDP-43 proteinopathy.

View Article: PubMed Central - PubMed

Affiliation: Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Taipei, Taiwan, ROC.

ABSTRACT
TDP-43 is a pathogenic protein: its normal function in binding to UG-rich RNA is related to cystic fibrosis, and inclusion of its C-terminal fragments in brain cells is directly linked to frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Here we report the 1.65 A crystal structure of the C-terminal RRM2 domain of TDP-43 in complex with a single-stranded DNA. We show that TDP-43 is a dimeric protein with two RRM domains, both involved in DNA and RNA binding. The crystal structure reveals the basis of TDP-43's TG/UG preference in nucleic acids binding. It also reveals that RRM2 domain has an atypical RRM-fold with an additional beta-strand involved in making protein-protein interactions. This self association of RRM2 domains produced thermal-stable RRM2 assemblies with a melting point greater than 85 degrees C as monitored by circular dichroism at physiological conditions. These studies thus characterize the recognition between TDP-43 and nucleic acids and the mode of RRM2 self association, and provide molecular models for understanding the role of TDP-43 in cystic fibrosis and the neurodegenerative diseases related to TDP-43 proteinopathy.

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Comparison of RRM domain assembly between TDP-43, hnRNP A1 and HuD. (A) The RRM2 domain of TDP-43 (in red) was superimposed onto the RRM2 of hnRNP A1. hnRNP A1 is a homodimer (in yellow and gray) bound to two strands of RNA (schematically displayed as a navy blue tube). The DNA bound to TDP-43 is displayed in green. (B) The RRM2 of TDP-43 (red) was superimposed onto the RRM2 of HuD (yellow). All the RRM2 domains in hnRNP A1, HuD and TDP-43 were fixed in the same orientation as marked by a black frame. (C) The dimeric interface in the TDP-43 RRM2 dimer is atypical, compared to those found in hnRNP A1 and HuD. (D) A similar T3-binding pocket was identified in several RRM proteins: TDP-43 in red (bound to T3); hnRNP A1 in navy blue (bound to A209); HuD in green (bound to U3); and Sxl in orange (bound to G4). (E) A similar G4 binding pocket in TDP-43 (in red) was only identified in hnRNP A1 (in navy blue, bound to G210). The PDB entry codes of the structures used in this figure are: 1U1O for hnRNP A1, 1FXL for HuD and 1B7F for Sxl.
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Figure 7: Comparison of RRM domain assembly between TDP-43, hnRNP A1 and HuD. (A) The RRM2 domain of TDP-43 (in red) was superimposed onto the RRM2 of hnRNP A1. hnRNP A1 is a homodimer (in yellow and gray) bound to two strands of RNA (schematically displayed as a navy blue tube). The DNA bound to TDP-43 is displayed in green. (B) The RRM2 of TDP-43 (red) was superimposed onto the RRM2 of HuD (yellow). All the RRM2 domains in hnRNP A1, HuD and TDP-43 were fixed in the same orientation as marked by a black frame. (C) The dimeric interface in the TDP-43 RRM2 dimer is atypical, compared to those found in hnRNP A1 and HuD. (D) A similar T3-binding pocket was identified in several RRM proteins: TDP-43 in red (bound to T3); hnRNP A1 in navy blue (bound to A209); HuD in green (bound to U3); and Sxl in orange (bound to G4). (E) A similar G4 binding pocket in TDP-43 (in red) was only identified in hnRNP A1 (in navy blue, bound to G210). The PDB entry codes of the structures used in this figure are: 1U1O for hnRNP A1, 1FXL for HuD and 1B7F for Sxl.

Mentions: About 2% of the gene products in humans contain at least one RNA recognition motif (RRM), making RRM one of the most abundant protein domains (23). Most RRM proteins have two to six copies of RRMs, which are folded into an αβ sandwich structure with a four β-stranded pleated sheet packed against two α-helices. Crystal structures of a number of RRM proteins containing two tandem RRM motifs, in a way similar to TDP-43, have been reported, including hnRNP A1 (27,28), Hud (29), Sxl (30), PABP (31) and FIR (32). hnRNP A1 forms a dimer when it is bound with single-stranded nucleic acids, whereas Hud, Sxl and PABP are monomers with similar relative domain arrangement between RRM1 and RRM2. The superposition of TDP-43 RRM2 domain onto the RRM2 domain of two representative RRM proteins, hnRNP A1 dimer (PDB entry code: 1U1O) and Hud monomer (PDB entry code: 1FXL), showed that the RRM2 domains in these proteins share a similar RRM fold, except that TDP-43 RRM2 has an extra β4 strand that is absent in hnRNP A1 and Hud (Figure 7).Figure 7.


Structural insights into TDP-43 in nucleic-acid binding and domain interactions.

Kuo PH, Doudeva LG, Wang YT, Shen CK, Yuan HS - Nucleic Acids Res. (2009)

Comparison of RRM domain assembly between TDP-43, hnRNP A1 and HuD. (A) The RRM2 domain of TDP-43 (in red) was superimposed onto the RRM2 of hnRNP A1. hnRNP A1 is a homodimer (in yellow and gray) bound to two strands of RNA (schematically displayed as a navy blue tube). The DNA bound to TDP-43 is displayed in green. (B) The RRM2 of TDP-43 (red) was superimposed onto the RRM2 of HuD (yellow). All the RRM2 domains in hnRNP A1, HuD and TDP-43 were fixed in the same orientation as marked by a black frame. (C) The dimeric interface in the TDP-43 RRM2 dimer is atypical, compared to those found in hnRNP A1 and HuD. (D) A similar T3-binding pocket was identified in several RRM proteins: TDP-43 in red (bound to T3); hnRNP A1 in navy blue (bound to A209); HuD in green (bound to U3); and Sxl in orange (bound to G4). (E) A similar G4 binding pocket in TDP-43 (in red) was only identified in hnRNP A1 (in navy blue, bound to G210). The PDB entry codes of the structures used in this figure are: 1U1O for hnRNP A1, 1FXL for HuD and 1B7F for Sxl.
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Figure 7: Comparison of RRM domain assembly between TDP-43, hnRNP A1 and HuD. (A) The RRM2 domain of TDP-43 (in red) was superimposed onto the RRM2 of hnRNP A1. hnRNP A1 is a homodimer (in yellow and gray) bound to two strands of RNA (schematically displayed as a navy blue tube). The DNA bound to TDP-43 is displayed in green. (B) The RRM2 of TDP-43 (red) was superimposed onto the RRM2 of HuD (yellow). All the RRM2 domains in hnRNP A1, HuD and TDP-43 were fixed in the same orientation as marked by a black frame. (C) The dimeric interface in the TDP-43 RRM2 dimer is atypical, compared to those found in hnRNP A1 and HuD. (D) A similar T3-binding pocket was identified in several RRM proteins: TDP-43 in red (bound to T3); hnRNP A1 in navy blue (bound to A209); HuD in green (bound to U3); and Sxl in orange (bound to G4). (E) A similar G4 binding pocket in TDP-43 (in red) was only identified in hnRNP A1 (in navy blue, bound to G210). The PDB entry codes of the structures used in this figure are: 1U1O for hnRNP A1, 1FXL for HuD and 1B7F for Sxl.
Mentions: About 2% of the gene products in humans contain at least one RNA recognition motif (RRM), making RRM one of the most abundant protein domains (23). Most RRM proteins have two to six copies of RRMs, which are folded into an αβ sandwich structure with a four β-stranded pleated sheet packed against two α-helices. Crystal structures of a number of RRM proteins containing two tandem RRM motifs, in a way similar to TDP-43, have been reported, including hnRNP A1 (27,28), Hud (29), Sxl (30), PABP (31) and FIR (32). hnRNP A1 forms a dimer when it is bound with single-stranded nucleic acids, whereas Hud, Sxl and PABP are monomers with similar relative domain arrangement between RRM1 and RRM2. The superposition of TDP-43 RRM2 domain onto the RRM2 domain of two representative RRM proteins, hnRNP A1 dimer (PDB entry code: 1U1O) and Hud monomer (PDB entry code: 1FXL), showed that the RRM2 domains in these proteins share a similar RRM fold, except that TDP-43 RRM2 has an extra β4 strand that is absent in hnRNP A1 and Hud (Figure 7).Figure 7.

Bottom Line: The crystal structure reveals the basis of TDP-43's TG/UG preference in nucleic acids binding.It also reveals that RRM2 domain has an atypical RRM-fold with an additional beta-strand involved in making protein-protein interactions.These studies thus characterize the recognition between TDP-43 and nucleic acids and the mode of RRM2 self association, and provide molecular models for understanding the role of TDP-43 in cystic fibrosis and the neurodegenerative diseases related to TDP-43 proteinopathy.

View Article: PubMed Central - PubMed

Affiliation: Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Taipei, Taiwan, ROC.

ABSTRACT
TDP-43 is a pathogenic protein: its normal function in binding to UG-rich RNA is related to cystic fibrosis, and inclusion of its C-terminal fragments in brain cells is directly linked to frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Here we report the 1.65 A crystal structure of the C-terminal RRM2 domain of TDP-43 in complex with a single-stranded DNA. We show that TDP-43 is a dimeric protein with two RRM domains, both involved in DNA and RNA binding. The crystal structure reveals the basis of TDP-43's TG/UG preference in nucleic acids binding. It also reveals that RRM2 domain has an atypical RRM-fold with an additional beta-strand involved in making protein-protein interactions. This self association of RRM2 domains produced thermal-stable RRM2 assemblies with a melting point greater than 85 degrees C as monitored by circular dichroism at physiological conditions. These studies thus characterize the recognition between TDP-43 and nucleic acids and the mode of RRM2 self association, and provide molecular models for understanding the role of TDP-43 in cystic fibrosis and the neurodegenerative diseases related to TDP-43 proteinopathy.

Show MeSH
Related in: MedlinePlus