25MN

Lysine racemase TM1597

Summary for 25MN

• Entry DOI: 10.2210/pdb25mn/pdb
• Descriptor: Lysine racemase (2 entities in total)
• Functional Keywords: plp-dependent enzyme, alanine racemase, isomerase
• Biological source: Thermotoga maritima MSB8
• Total number of polymer chains: 6
• Total formula weight: 248086.55

Authors

Nitta, S.,Miyamoto, T.,Fushinobu, S. (deposition date: 2026-04-09, release date: 2026-10-07, Last modification date: 2026-10-14)

Primary citation

Miyamoto, T.,Moriya, T.,Nitta, S.,Fushinobu, S.
Elucidation of d-alanine biosynthetic pathways in the hyperthermophiles: Characterization of alanine racemase from Thermus thermophilus and the structure and dual physiological functions of lysine racemase from Thermotoga maritima.
Arch.Biochem.Biophys., 786:111010-111010, 2026

PubMed Abstract: The hyperthermophilic bacterium Thermotoga maritima contains a peptidoglycan comprising d-alanine, d-glutamate, and d-lysine. We have previously identified the biosynthetic pathways of d-lysine and d-glutamate; however, the biosynthetic pathway of d-alanine is unclear in T. maritima. The present study elucidated the d-alanine biosynthetic pathway in T. maritima, following the characterization of the TTHA0062 activity, constructed a TTHA0062 (encoding alanine racemase)-deficient Thermus thermophilus (ΔTTHA0062) strain. TTHA0062 exhibited the racemase activity toward 10 amino acids including Ala, and the catalytic efficiency of l-alanine was twofold higher than that of d-alanine. Regarding the T. maritima genes introduced into the genome of the ΔTTHA0062 strain, TM1597 (lysine racemase) completely restored the growth, TM1270 (multifunctional enzyme) resulted in partial restoration, whereas TM0831 (d-amino acid aminotransferase) had no effect, suggesting that TM1597 and TM1270 are involved in d-alanine biosynthesis in T. maritima. Furthermore, we determined the crystal structure of TM1597 in the internal aldimine form, in which pyridoxal 5'-phosphate (PLP) forms a Schiff base linkage with the active site residue Lys36, and revealed the residues crucial for the catalytic reaction by TM1597 mutational analysis.

PubMed: 42767480
DOI: 10.1016/j.abb.2026.111010

Experimental method

X-RAY DIFFRACTION (2.15 Å)