Limits...
DNA3'pp5'G de-capping activity of aprataxin: effect of cap nucleoside analogs and structural basis for guanosine recognition.

Chauleau M, Jacewicz A, Shuman S - Nucleic Acids Res. (2015)

Bottom Line: We report a 1.5 Å crystal structure of aprataxin in a complex with GMP, which reveals that: (i) GMP binds at the same position and in the same anti nucleoside conformation as AMP; and (ii) aprataxin makes more extensive nucleobase contacts with guanine than with adenine, via a hydrogen bonding network to the guanine O6, N1, N2 base edge.Alanine mutations of catalytic residues His147 and His149 abolish DNAppG de-capping activity, suggesting that the 3' de-guanylylation and 5' de-adenylylation reactions follow the same pathway of nucleotidyl transfer through a covalent aprataxin-(His147)-NMP intermediate.Alanine mutation of Asp63, which coordinates the guanosine ribose hydroxyls, impairs DNAppG de-capping.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA.

Show MeSH

Related in: MedlinePlus

Aprataxin·DNA complex. Stereo view of the interface of aprataxin with the 10-mer DNA (stick model with gray carbons) in the presently solved complex in space group P321. Relevant protein side chain and main chain atoms are depicted as stick models with beige carbons. Atomic contacts to the phosphodiester backbone are denoted by dashed lines.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4499129&req=5

Figure 7: Aprataxin·DNA complex. Stereo view of the interface of aprataxin with the 10-mer DNA (stick model with gray carbons) in the presently solved complex in space group P321. Relevant protein side chain and main chain atoms are depicted as stick models with beige carbons. Atomic contacts to the phosphodiester backbone are denoted by dashed lines.

Mentions: In brief, the aprataxin-DNA interface in the present structure spans 8-nt (Figure 7). The duplex end is bookmarked by Phe34, which makes a π-stack on the guanine nucleobase of the 5′ G:C base pair. Phe65 packs again the penultimate ribose of the substrate strand. All other contacts are with the phosphate backbone. Lys67 and His165 coordinate the terminal phosphodiester of the substrate strand and Lys161 coordinates the second phosphodiester. Distal atomic contacts to the template strand are via the Zn-finger domain. Arg209 makes a bidentate interaction with the sixth phosphodiester. The seventh phosphodiester is engaged by the Phe211 and Thr212 main-chain amides. The eight phosphodiester receives a hydrogen bond from by the Thr212 side chain (Figure 7).


DNA3'pp5'G de-capping activity of aprataxin: effect of cap nucleoside analogs and structural basis for guanosine recognition.

Chauleau M, Jacewicz A, Shuman S - Nucleic Acids Res. (2015)

Aprataxin·DNA complex. Stereo view of the interface of aprataxin with the 10-mer DNA (stick model with gray carbons) in the presently solved complex in space group P321. Relevant protein side chain and main chain atoms are depicted as stick models with beige carbons. Atomic contacts to the phosphodiester backbone are denoted by dashed lines.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4499129&req=5

Figure 7: Aprataxin·DNA complex. Stereo view of the interface of aprataxin with the 10-mer DNA (stick model with gray carbons) in the presently solved complex in space group P321. Relevant protein side chain and main chain atoms are depicted as stick models with beige carbons. Atomic contacts to the phosphodiester backbone are denoted by dashed lines.
Mentions: In brief, the aprataxin-DNA interface in the present structure spans 8-nt (Figure 7). The duplex end is bookmarked by Phe34, which makes a π-stack on the guanine nucleobase of the 5′ G:C base pair. Phe65 packs again the penultimate ribose of the substrate strand. All other contacts are with the phosphate backbone. Lys67 and His165 coordinate the terminal phosphodiester of the substrate strand and Lys161 coordinates the second phosphodiester. Distal atomic contacts to the template strand are via the Zn-finger domain. Arg209 makes a bidentate interaction with the sixth phosphodiester. The seventh phosphodiester is engaged by the Phe211 and Thr212 main-chain amides. The eight phosphodiester receives a hydrogen bond from by the Thr212 side chain (Figure 7).

Bottom Line: We report a 1.5 Å crystal structure of aprataxin in a complex with GMP, which reveals that: (i) GMP binds at the same position and in the same anti nucleoside conformation as AMP; and (ii) aprataxin makes more extensive nucleobase contacts with guanine than with adenine, via a hydrogen bonding network to the guanine O6, N1, N2 base edge.Alanine mutations of catalytic residues His147 and His149 abolish DNAppG de-capping activity, suggesting that the 3' de-guanylylation and 5' de-adenylylation reactions follow the same pathway of nucleotidyl transfer through a covalent aprataxin-(His147)-NMP intermediate.Alanine mutation of Asp63, which coordinates the guanosine ribose hydroxyls, impairs DNAppG de-capping.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA.

Show MeSH
Related in: MedlinePlus