1DEK

DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE COMPLEXED WITH DEOXY-GMP

1DEK の概要

• エントリーDOI: 10.2210/pdb1dek/pdb
• 分子名称: DEOXYNUCLEOSIDE MONOPHOSPHATE KINASE, MAGNESIUM ION, 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE, ... (4 entities in total)
• 機能のキーワード: transferase, phosphotransferase
• 由来する生物種: Enterobacteria phage T4
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 55557.27

構造登録者

Teplyakov, A.,Sebastiao, P. (登録日: 1996-01-09, 公開日: 1997-01-11, 最終更新日: 2024-06-05)

主引用文献

Teplyakov, A.,Sebastiao, P.,Obmolova, G.,Perrakis, A.,Brush, G.S.,Bessman, M.J.,Wilson, K.S.
Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.
EMBO J., 15:3487-3497, 1996

PubMed Abstract: NMP kinases catalyse the phosphorylation of the canonical nucleotides to the corresponding diphosphates using ATP as a phosphate donor. Bacteriophage T4 deoxynucleotide kinase (DNK) is the only member of this family of enzymes that recognizes three structurally dissimilar nucleotides: dGMP, dTMP and 5-hydroxymethyl-dCMP while excluding dCMP and dAMP. The crystal structure of DNK with its substrate dGMP has been determined at 2.0 A resolution by single isomorphous replacement. The structure of the ternary complex with dGMP and ATP has been determined at 2.2 A resolution. The polypeptide chain of DNK is folded into two domains of equal size, one of which resembles the mononucleotide binding motif with the glycine-rich P-loop. The second domain, consisting of five alpha-helices, forms the NMP binding pocket. A hinge connection between the domains allows for large movements upon substrate binding which are not restricted by dimerization of the enzyme. The mechanism of active centre formation via domain closure is described. Comparison with other P-loop-containing proteins indicates an induced-fit mode of NTP binding. Protein-substrate interactions observed at the NMP and NTP sites provide the basis for understanding the principles of nucleotide discrimination.

PubMed: 8670851

実験手法

X-RAY DIFFRACTION (2 Å)