5XPF

High-resolution X-ray structure of the T26H mutant of T4 lysozyme

Summary for 5XPF

• Entry DOI: 10.2210/pdb5xpf/pdb
• Related: 1QT8
• Descriptor: Endolysin, SODIUM ION, CHLORIDE ION, ... (6 entities in total)
• Functional Keywords: alpha and beta protein, hydrolase, t26h mutant, perdeuterated protein
• Biological source: Enterobacteria phage T4
• Cellular location: Host cytoplasm : D9IEF7
• Total number of polymer chains: 1
• Total formula weight: 19660.62

Authors

Hiromoto, T.,Kuroki, R. (deposition date: 2017-06-01, release date: 2017-10-04, Last modification date: 2023-11-22)

Primary citation

Hiromoto, T.,Meilleur, F.,Shimizu, R.,Shibazaki, C.,Adachi, M.,Tamada, T.,Kuroki, R.
Neutron structure of the T26H mutant of T4 phage lysozyme provides insight into the catalytic activity of the mutant enzyme and how it differs from that of wild type.
Protein Sci., 26:1953-1963, 2017

PubMed Abstract: T4 phage lysozyme is an inverting glycoside hydrolase that degrades the murein of bacterial cell walls by cleaving the β-1,4-glycosidic bond. The substitution of the catalytic Thr26 residue to a histidine converts the wild type from an inverting to a retaining enzyme, which implies that the original general acid Glu11 can also act as an acid/base catalyst in the hydrolysis. Here, we have determined the neutron structure of the perdeuterated T26H mutant to clarify the protonation states of Glu11 and the substituted His26, which are key in the retaining reaction. The 2.09-Å resolution structure shows that the imidazole group of His26 is in its singly protonated form in the active site, suggesting that the deprotonated Nɛ2 atom of His26 can attack the anomeric carbon of bound substrate as a nucleophile. The carboxyl group of Glu11 is partially protonated and interacts with the unusual neutral state of the guanidine moiety of Arg145, as well as two heavy water molecules. Considering that one of the water-binding sites has the potential to be occupied by a hydronium ion, the bulk solvent could be the source for the protonation of Glu11. The respective protonation states of Glu11 and His26 are consistent with the bond lengths determined by an unrestrained refinement of the high-resolution X-ray structure of T26H at 1.04-Å resolution. The detail structural information, including the coordinates of the deuterium atoms in the active site, provides insight into the distinctively different catalytic activities of the mutant and wild type enzymes.

PubMed: 28707339
DOI: 10.1002/pro.3230

Experimental method

X-RAY DIFFRACTION (1.04 Å)