3TMK

CRYSTAL STRUCTURE OF YEAST THYMIDYLATE KINASE COMPLEXED WITH THE BISUBSTRATE INHIBITOR TP5A AT 2.0 A RESOLUTION: IMPLICATIONS FOR CATALYSIS AND AZT ACTIVATION

3TMK の概要

• エントリーDOI: 10.2210/pdb3tmk/pdb
• 分子名称: THYMIDYLATE KINASE, P1-(5'-ADENOSYL)P5-(5'-THYMIDYL)PENTAPHOSPHATE (3 entities in total)
• 機能のキーワード: kinase, phosphotransferase
• 由来する生物種: Saccharomyces cerevisiae (baker's yeast)
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 204885.83

構造登録者

Lavie, A.,Schlichting, I.,Konrad, M.,Goody, R.S.,Brundiers, R.,Reinstein, J. (登録日: 1998-01-26, 公開日: 1999-02-16, 最終更新日: 2024-05-22)

主引用文献

Lavie, A.,Konrad, M.,Brundiers, R.,Goody, R.S.,Schlichting, I.,Reinstein, J.
Crystal structure of yeast thymidylate kinase complexed with the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-thymidyl) pentaphosphate (TP5A) at 2.0 A resolution: implications for catalysis and AZT activation.
Biochemistry, 37:3677-3686, 1998

PubMed Abstract: The crystal structure of yeast thymidylate kinase (TmpK) complexed with the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-thymidyl) pentaphosphate (TP5A) was determined at 2.0 A resolution. In this complex, TmpK adopts a closed conformation with a region (LID) of the protein closing upon the substrate and forming a helix. The interactions of TmpK and TP5A strongly suggest that arginine 15, which is located in the phosphate binding loop (P-loop) sequence, plays a catalytic role by interacting with an oxygen atom of the transferred phosphoryl group. Unlike other nucleoside monophosphate kinases where basic residues from the LID region participate in stabilizing the transition state, TmpK lacks such residues in the LID region. We attribute this function to Arg 15 of the P-loop. TmpK plays an important role in the phosphorylation of the AIDS prodrug AZT. The structures of TmpK with dTMP and with AZT-MP [Lavie, A., et al. (1997) Nat. Struct. Biol. 4, 601-604] implicate the movement of Arg15 in response to AZT-MP binding as an important factor in the 200-fold reduced catalytic rate with AZT-MP. TmpK from Escherichia coli lacks this arginine in its P-loop while having basic residues in the LID region. This suggested that, if such a P-loop movement were to occur in the E. coli TmpK upon AZT-MP binding, it should not have such a detrimental effect on catalysis. This hypothesis was tested, and as postulated, E. coli TmpK phosphorylates AZT-MP only 2.5 times slower than dTMP.

PubMed: 9521686
DOI: 10.1021/bi9720787

実験手法

X-RAY DIFFRACTION (2 Å)