4YKL

Hnt3 in complex with DNA and guanosine

Summary for 4YKL

• Entry DOI: 10.2210/pdb4ykl/pdb
• Descriptor: Aprataxin-like protein, DNA (5'-D(*GP*AP*AP*TP*CP*AP*TP*AP*AP*C)-3'), ZINC ION, ... (7 entities in total)
• Functional Keywords: gmp, nucleotidyl transferase, hydrolase, hydrolase-dna complex, hydrolase/dna
• Biological source: Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast); More
• Total number of polymer chains: 2
• Total formula weight: 27051.61

Authors

Jacewicz, A.,Chauleau, M.,Shuman, S. (deposition date: 2015-03-04, release date: 2015-06-03, Last modification date: 2023-09-27)

Primary citation

Chauleau, M.,Jacewicz, A.,Shuman, S.
DNA3'pp5'G de-capping activity of aprataxin: effect of cap nucleoside analogs and structural basis for guanosine recognition.
Nucleic Acids Res., 43:6075-6083, 2015

PubMed Abstract: DNA3'pp5'G caps synthesized by the 3'-PO4/5'-OH ligase RtcB have a strong impact on enzymatic reactions at DNA 3'-OH ends. Aprataxin, an enzyme that repairs A5'pp5'DNA ends formed during abortive ligation by classic 3'-OH/5'-PO4 ligases, is also a DNA 3' de-capping enzyme, converting DNAppG to DNA3'p and GMP. By taking advantage of RtcB's ability to utilize certain GTP analogs to synthesize DNAppN caps, we show that aprataxin hydrolyzes inosine and 6-O-methylguanosine caps, but is not adept at removing a deoxyguanosine cap. 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.

PubMed: 26007660
DOI: 10.1093/nar/gkv501

Experimental method

X-RAY DIFFRACTION (2.25 Å)