8HIC

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

Summary for 8HIC

• Entry DOI: 10.2210/pdb8hic/pdb
• Descriptor: Putative urea ABC transporter, substrate binding protein, UREA, CALCIUM ION, ... (4 entities in total)
• Functional Keywords: transporter, complex, urea, urta, transport protein
• Biological source: Prochlorococcus marinus str. MIT 9313
• Total number of polymer chains: 1
• Total formula weight: 45872.24

Authors

Zhang, Y.Z.,Wang, P.,Wang, C. (deposition date: 2022-11-19, release date: 2023-11-22, Last modification date: 2024-11-20)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.6 Å)