9DUC

Wild-Type E. coli Glucokinase

Summary for 9DUC

• Entry DOI: 10.2210/pdb9duc/pdb
• Descriptor: Glucokinase, PHOSPHATE ION (3 entities in total)
• Functional Keywords: metabolic role, transferase
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 71379.74

Authors

Andrews, J.R.W.,Sakon, J.,Fan, C. (deposition date: 2024-10-02, release date: 2025-08-06, Last modification date: 2025-10-22)

Primary citation

Andrews, J.,Sakon, J.,Fan, C.
Crystal structures of Escherichia coli glucokinase and insights into phosphate binding.
Acta Crystallogr.,Sect.F, 81:332-337, 2025

PubMed Abstract: Here, we report the crystal structure of Escherichia coli glucokinase (GLK), which has phosphate bound in the cleft between the α and β domains adjacent to the active site. A ternary complex consisting of GLK, glucose and phosphate is also reported in this work. Diffraction data were collected at 2.63 Å resolution for the phospate-bound form (R/R = 0.191/0.230) and at 2.54 Å resolution for the ternary complex (R/R = 0.202/0.258), both at 297 K. A B-factor analysis of the phosphate-bound GLK structure revealed consistently lower values for phosphate-interacting basic residues in the α4, α5 and α9 helices, while significant root-mean-square deviation (r.m.s.d.) spikes indicated flexibility in regions preceding β1 and within the loop between the β5 and β6 sheets of the α domain. In the ternary complex, phosphate is bound adjacent to glucose, and the B factors for the α4, α5 and α9 helices were further reduced, while r.m.s.d. spikes were observed at the end of the β10 sheet and within the α6 helix of the β-domain. This structural characterization suggests that phosphate could influence the activity of GLK by altering glucose binding and modulating interactions with a loop-interacting regulatory protein.

PubMed: 40632113
DOI: 10.1107/S2053230X25005515

Experimental method

X-RAY DIFFRACTION (2.63 Å)