8JBD

Crystal structure of Adenylosuccinate lyase from Thermus thermophilus HB8, TtPurB

8JBD の概要

• エントリーDOI: 10.2210/pdb8jbd/pdb
• 分子名称: Adenylosuccinate lyase (2 entities in total)
• 機能のキーワード: adenylosuccinate lyase purine biosynthesis thermus thermophilus, lyase
• 由来する生物種: Thermus thermophilus HB8
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 102518.82

構造登録者

Nemoto, N.,Kawai, G.,Sampei, G. (登録日: 2023-05-08, 公開日: 2023-11-15)

主引用文献

Nemoto, N.,Kawai, G.,Sampei, G.I.
Crystal structure of adenylosuccinate lyase from the thermophilic bacterium Thermus thermophilus HB8.
Acta Crystallogr.,Sect.F, 79:278-284, 2023

PubMed Abstract: Adenylosuccinate lyase (PurB) catalyzes two distinct reactions in the purine nucleotide biosynthetic pathway using the same active site. The ability to recognize two different sets of substrates is of structural and evolutionary interest. In the present study, the crystal structure of PurB from the thermophilic bacterium Thermus thermophilus HB8 (TtPurB) was determined at a resolution of 2.38 Å by molecular replacement using a structure predicted by AlphaFold2 as a template. The asymmetric unit of the TtPurB crystal contained two TtPurB molecules, and some regions were disordered in the crystal structure. The disordered regions were the substrate-binding site and domain 3. TtPurB forms a homotetramer and the monomer is composed of three domains (domains 1, 2 and 3), which is a typical structure for the aspartase/fumarase superfamily. Molecular dynamics simulations with and without substrate/product were performed using a full-length model of TtPurB which was obtained before deletion of the disordered regions. The substrates and products were bound to the model structures during the MD simulations. The fluctuations of amino-acid residues were greater in the disordered regions and became smaller upon the binding of substrate or product. These results demonstrate that the full-length model obtained using AlphaFold2 can be used to generate the coordinates of disordered regions within the crystal structure.

PubMed: 37873935
DOI: 10.1107/S2053230X23009020

実験手法

X-RAY DIFFRACTION (2.38 Å)