Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

8Z79

Crystal structure of 5-N-alpha-glycinylthymidine (N-alpha-GlyT) FAD-dependent lyase gp47/NGTO from Pseudomonas phage PaMx11 in complex with dsDNA

Summary for 8Z79
Entry DOI10.2210/pdb8z79/pdb
DescriptorFlavin-dependent lyase, DNA (5'-D(*TP*AP*GP*TP*CP*AP*TP*GP*AP*CP*T)-3'), FLAVIN-ADENINE DINUCLEOTIDE (3 entities in total)
Functional Keywordsn-alpha-glyt, hypermodification, dna, complex, pseudomonads phage, ngto, fad, oxidoreductase/dna, oxidoreductase-dna complex
Biological sourcePseudomonas phage PaMx11
More
Total number of polymer chains8
Total formula weight139731.24
Authors
Wen, Y.,Guo, W.T.,Wu, B.X. (deposition date: 2024-04-19, release date: 2024-10-02, Last modification date: 2024-10-30)
Primary citationWen, Y.,Guo, W.,Meng, C.,Yang, J.,Xu, S.,Chen, H.,Gan, J.,Wu, B.
Structural insights into the biosynthetic mechanism of N alpha-GlyT and 5-NmdU hypermodifications of DNA.
Nucleic Acids Res., 52:11083-11097, 2024
Cited by
PubMed Abstract: DNA hypermodifications are effective weapons for phages to cope with the defense system of bacteria. The biogenesis of DNA hypermodification in phages involves multiple steps, from the modified deoxynucleotide monophosphates to the final hypermodification on the DNA chains. PseudomonasPaMx11 gp46 and gp47 encode the enzymes for sequentially converting 5-phosphomethyl-2'-deoxyuridine to 5-Nα-glycinylthymidine and 5-aminomethyl-2'-deoxyuridine. Here, we have determined the crystal structures of gp46 and gp47 in their apo and double-stranded DNA (dsDNA)-bound forms. We uncovered their dsDNA recognition properties and identified the critical residues for the catalytic reactions. Combined with in vitro biochemical studies, we proposed a plausible reaction scheme for gp46 and gp47 in converting these DNA hypermodifications. Our studies will provide the structural basis for future bioengineering of the synthetic pathway of hypermodification and identifying new modifications in mammals by enzyme-assisted sequencing methods.
PubMed: 39268585
DOI: 10.1093/nar/gkae784
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.65 Å)
Structure validation

227111

PDB entries from 2024-11-06

PDB statisticsPDBj update infoContact PDBjnumon