2ICY

Crystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UDP-glucose

2ICY の概要

• エントリーDOI: 10.2210/pdb2icy/pdb
• 関連するPDBエントリー: 1Z90 2ICX
• 分子名称: Probable UTP-glucose-1-phosphate uridylyltransferase 2, DIMETHYL SULFOXIDE, URIDINE-5'-DIPHOSPHATE-GLUCOSE, ... (5 entities in total)
• 機能のキーワード: at3g03250, udp, putative udp-glucose pyrophosphorylase, structural genomics functional follow-up study, structural genomics, protein structure initiative, psi, cesg, center for eukaryotic structural genomics, transferase
• 由来する生物種: Arabidopsis thaliana (thale cress)
• 細胞内の位置: Cytoplasm (By similarity): Q9M9P3
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 105043.10

構造登録者

McCoy, J.G.,Wesenberg, G.E.,Phillips Jr., G.N.,Bitto, E.,Bingman, C.A.,Center for Eukaryotic Structural Genomics (CESG) (登録日: 2006-09-13, 公開日: 2006-10-03, 最終更新日: 2023-08-30)

主引用文献

McCoy, J.G.,Bitto, E.,Bingman, C.A.,Wesenberg, G.E.,Bannen, R.M.,Kondrashov, D.A.,Phillips Jr., G.N.
Structure and Dynamics of UDP-Glucose Pyrophosphorylase from Arabidopsis thaliana with Bound UDP-Glucose and UTP.
J.Mol.Biol., 366:830-841, 2007

PubMed Abstract: The structure of the UDP-glucose pyrophosphorylase encoded by Arabidopsis thaliana gene At3g03250 has been solved to a nominal resolution of 1.86 Angstroms. In addition, the structure has been solved in the presence of the substrates/products UTP and UDP-glucose to nominal resolutions of 1.64 Angstroms and 1.85 Angstroms. The three structures revealed a catalytic domain similar to that of other nucleotidyl-glucose pyrophosphorylases with a carboxy-terminal beta-helix domain in a unique orientation. Conformational changes are observed between the native and substrate-bound complexes. The nucleotide-binding loop and the carboxy-terminal domain, including the suspected catalytically important Lys360, move in and out of the active site in a concerted fashion. TLS refinement was employed initially to model conformational heterogeneity in the UDP-glucose complex followed by the use of multiconformer refinement for the entire molecule. Normal mode analysis generated atomic displacement predictions in good agreement in magnitude and direction with the observed conformational changes and anisotropic displacement parameters generated by TLS refinement. The structures and the observed dynamic changes provide insight into the ordered mechanism of this enzyme and previously described oligomerization effects on catalytic activity.

PubMed: 17178129
DOI: 10.1016/j.jmb.2006.11.059

実験手法

X-RAY DIFFRACTION (1.64 Å)