3JPZ

Crystal Structure of Lombricine Kinase

3JPZ の概要

• エントリーDOI: 10.2210/pdb3jpz/pdb
• 関連するPDBエントリー: 3jq3
• 分子名称: Lombricine kinase, NITRATE ION (3 entities in total)
• 機能のキーワード: mixed alpha / beta, kinase, transferase
• 由来する生物種: Urechis caupo (Innkeeper worm)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 82307.03

構造登録者

Bush, D.J.,Kirillova, O.,Clark, S.A.,Fabiola, F.,Somasundaram, T.,Chapman, M.S. (登録日: 2009-09-04, 公開日: 2010-09-15, 最終更新日: 2023-09-06)

主引用文献

Bush, D.J.,Kirillova, O.,Clark, S.A.,Davulcu, O.,Fabiola, F.,Xie, Q.,Somasundaram, T.,Ellington, W.R.,Chapman, M.S.
The structure of lombricine kinase: implications for phosphagen kinase conformational changes.
J.Biol.Chem., 286:9338-9350, 2011

PubMed Abstract: Lombricine kinase is a member of the phosphagen kinase family and a homolog of creatine and arginine kinases, enzymes responsible for buffering cellular ATP levels. Structures of lombricine kinase from the marine worm Urechis caupo were determined by x-ray crystallography. One form was crystallized as a nucleotide complex, and the other was substrate-free. The two structures are similar to each other and more similar to the substrate-free forms of homologs than to the substrate-bound forms of the other phosphagen kinases. Active site specificity loop 309-317, which is disordered in substrate-free structures of homologs and is known from the NMR of arginine kinase to be inherently dynamic, is resolved in both lombricine kinase structures, providing an improved basis for understanding the loop dynamics. Phosphagen kinases undergo a segmented closing on substrate binding, but the lombricine kinase ADP complex is in the open form more typical of substrate-free homologs. Through a comparison with prior complexes of intermediate structure, a correlation was revealed between the overall enzyme conformation and the substrate interactions of His(178). Comparative modeling provides a rationale for the more relaxed specificity of these kinases, of which the natural substrates are among the largest of the phosphagen substrates.

PubMed: 21212263
DOI: 10.1074/jbc.M110.202796

実験手法

X-RAY DIFFRACTION (1.95 Å)