8YRU

Crystal structure of D-amino acid transaminase from Haliscomenobacter hydrossis (apo form) after 15 sec of soaking with phenylhydrazine

Summary for 8YRU

• Entry DOI: 10.2210/pdb8yru/pdb
• Descriptor: Aminotransferase class IV, ACETATE ION, [6-methyl-5-oxidanyl-4-[(2-phenylhydrazinyl)methyl]pyridin-3-yl]methyl dihydrogen phosphate, ... (4 entities in total)
• Functional Keywords: daat, apo form, transaminase, aminotransferase, d-amino acid, transferase
• Biological source: Haliscomenobacter hydrossis DSM 1100
• Total number of polymer chains: 1
• Total formula weight: 32718.11

Authors

Matyuta, I.O.,Bakunova, A.K.,Minyaev, M.E.,Popov, V.O.,Boyko, K.M. (deposition date: 2024-03-21, release date: 2024-04-17, Last modification date: 2024-10-30)

Primary citation

Bakunova, A.K.,Matyuta, I.O.,Minyaev, M.E.,Boyko, K.M.,Popov, V.O.,Bezsudnova, E.Y.
Incorporation of pyridoxal-5'-phosphate into the apoenzyme: A structural study of D-amino acid transaminase from Haliscomenobacter hydrossis.
Biochim Biophys Acta Proteins Proteom, 1873:141056-141056, 2024

PubMed Abstract: Pyridoxal-5'-phosphate (PLP)-dependent transaminases are key enzymes of amino acid metabolism in cells and remarkable biocatalysts of stereoselective amination for process chemistry applications. As cofactor-dependent enzymes, transaminases are prone to cofactor leakage. Here we discuss the holoenzyme-apoenzyme interconversion and the kinetics of PLP incorporation into the apo form of a PLP-dependent transaminase from Haliscomenobacter hydrossis. PLP binding to the apoenzyme was slow in buffer, but was accelerated in the presence of substrates. Two crystal structures of the apoenzyme were obtained: the directly obtained apoenzyme (PDB ID: 7P8O) and the one obtained by soaking crystals of the holoenzyme in a phenylhydrazine solution (PDB ID: 8YRU). The mechanism of PLP association with the apoenzyme was proposed on the basis of structural analysis of these apo forms. Three rearrangement steps, including (I) anchoring of the PLP via the phosphate group, (II) displacement of two loops, and (III) Schiff-bonding between the PLP and the ε-amino group of the catalytic lysine residue, reconstituted the active holo form of the transaminase from H. hydrossis. The results obtained allowed us to determine in the active site a permanent part and elements that are assembled by PLP, these findings may be useful for transaminase engineering for biocatalysis.

PubMed: 39406293
DOI: 10.1016/j.bbapap.2024.141056

Experimental method

X-RAY DIFFRACTION (2 Å)