8HIC

Crystal structure of UrtA from Prochlorococcus marinus str. MIT 9313 in complex with urea and calcium

8HIC の概要

• エントリーDOI: 10.2210/pdb8hic/pdb
• 分子名称: Putative urea ABC transporter, substrate binding protein, UREA, CALCIUM ION, ... (4 entities in total)
• 機能のキーワード: transporter, complex, urea, urta, transport protein
• 由来する生物種: Prochlorococcus marinus str. MIT 9313
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 45872.24

構造登録者

Zhang, Y.Z.,Wang, P.,Wang, C. (登録日: 2022-11-19, 公開日: 2023-11-22, 最終更新日: 2024-11-20)

主引用文献

Wang, C.,Zhu, W.J.,Ding, H.T.,Liu, N.H.,Cao, H.Y.,Suo, C.L.,Liu, Z.K.,Zhang, Y.,Sun, M.L.,Fu, H.H.,Li, C.Y.,Chen, X.L.,Zhang, Y.Z.,Wang, P.
Structural and molecular basis for urea recognition by Prochlorococcus.
J.Biol.Chem., 299:104958-104958, 2023

PubMed Abstract: Nitrogen (N) is an essential element for microbial growth and metabolism. The growth and reproduction of microorganisms in more than 75% of areas of the ocean are limited by N. Prochlorococcus is numerically the most abundant photosynthetic organism on the planet. Urea is an important and efficient N source for Prochlorococcus. However, how Prochlorococcus recognizes and absorbs urea still remains unclear. Prochlorococcus marinus MIT 9313, a typical Cyanobacteria, contains an ABC-type transporter, UrtABCDE, which may account for the transport of urea. Here, we heterologously expressed and purified UrtA, the substrate-binding protein of UrtABCDE, detected its binding affinity toward urea, and further determined the crystal structure of the UrtA/urea complex. Molecular dynamics simulations indicated that UrtA can alternate between "open" and "closed" states for urea binding. Based on structural and biochemical analyses, the molecular mechanism for urea recognition and binding was proposed. When a urea molecule is bound, UrtA undergoes a state change from open to closed surrounding the urea molecule, and the urea molecule is further stabilized by the hydrogen bonds supported by the conserved residues around it. Moreover, bioinformatics analysis showed that ABC-type urea transporters are widespread in bacteria and probably share similar urea recognition and binding mechanisms as UrtA from P. marinus MIT 9313. Our study provides a better understanding of urea absorption and utilization in marine bacteria.

PubMed: 37380083
DOI: 10.1016/j.jbc.2023.104958

実験手法

X-RAY DIFFRACTION (1.6 Å)