8ZOV

The crystal structures of MurK in complex with glucose from Clostridium acetobutylicum

Summary for 8ZOV

• Entry DOI: 10.2210/pdb8zov/pdb
• Descriptor: N-acetylmuramic acid/N-acetylglucosamine kinase, beta-D-glucopyranose (3 entities in total)
• Functional Keywords: n-acetylmuramic acid/n-acetylglucosamine kinase, murk, nucleotide-binding, transferase
• Biological source: Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W)
• Total number of polymer chains: 1
• Total formula weight: 33652.97

Authors

Yang, X.Y.,Liu, X.H. (deposition date: 2024-05-29, release date: 2025-04-09)

Primary citation

He, X.,Liu, C.,Li, X.,Yang, Q.,Niu, F.,An, L.,Fan, Y.,Li, Y.,Zhou, Z.,Zhou, H.,Yang, X.,Liu, X.
Structural and biochemical insights into the molecular mechanism of N-acetylglucosamine/N-Acetylmuramic acid kinase MurK from Clostridium acetobutylicum.
Int.J.Biol.Macromol., 280:135747-135747, 2024

PubMed Abstract: MurK is a MurNAc- and GlcNAc-specific amino sugar kinase, phosphorylates MurNAc and GlcNAc at the 6-hydroxyl group in an ATP-dependent manner, and contributes to the recovery of both amino sugars during the cell wall turnover in Clostridium acetobutylicum. Herein, we determined the crystal structures of MurK in complex with MurNAc, GlcNAc, and glucose, respectively. MurK represents the V-shaped fold, which is divided into a small N-terminal domain and a large C-terminal domain. The catalytic pocket is located within the deep cavity between the two domains of the MurK monomer. We mapped the significant enzyme-substrate interactions, identified key residues involved in the catalytic activity of MurK, and found that residues Asp and Arg from the β4-α2-loop confer structural flexibilities to specifically accommodate GlcNAc and MurNAc, respectively. Moreover, structural comparison revealed that MurK adopts closed-active conformation induced by the N-acetyl moiety from GlcNAc/MurNAc, rather than closed-inactive conformation induced by glucose, to carry out its catalytic reaction. Taken together, our study provides structural and functional insights into the molecular mechanism of MurK for the phosphorylation of both MurNAc and GlcNAc, sugar substrate specificity, and conformational changes upon sugar substrate binding.

PubMed: 39304040
DOI: 10.1016/j.ijbiomac.2024.135747

Experimental method

X-RAY DIFFRACTION (1.42 Å)