6G58

Structure of the alanine racemase from Staphylococcus aureus in complex with a pyridoxal 5' phosphate-derivative

Summary for 6G58

• Entry DOI: 10.2210/pdb6g58/pdb
• Descriptor: Alanine racemase 1, (6-but-3-ynyl-4-methyl-5-oxidanyl-pyridin-3-yl)methyl dihydrogen phosphate, SODIUM ION, ... (9 entities in total)
• Functional Keywords: pyridoxal 5 phosphate dependent, d-alanine biosynthesis, biosynthetic protein
• Biological source: Staphylococcus aureus
• Total number of polymer chains: 2
• Total formula weight: 92797.33

Authors

Hoegl, A.,Sieber, S.A.,Schneider, S. (deposition date: 2018-03-29, release date: 2018-05-30, Last modification date: 2024-10-23)

Primary citation

Hoegl, A.,Nodwell, M.B.,Kirsch, V.C.,Bach, N.C.,Pfanzelt, M.,Stahl, M.,Schneider, S.,Sieber, S.A.
Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics.
Nat Chem, 10:1234-1245, 2018

PubMed Abstract: Pyridoxal phosphate (PLP) is an enzyme cofactor required for the chemical transformation of biological amines in many central cellular processes. PLP-dependent enzymes (PLP-DEs) are ubiquitous and evolutionarily diverse, making their classification based on sequence homology challenging. Here we present a chemical proteomic method for reporting on PLP-DEs using functionalized cofactor probes. We synthesized pyridoxal analogues modified at the 2'-position, which are taken up by cells and metabolized in situ. These pyridoxal analogues are phosphorylated to functional cofactor surrogates by cellular pyridoxal kinases and bind to PLP-DEs via an aldimine bond which can be rendered irreversible by NaBH reduction. Conjugation to a reporter tag enables the subsequent identification of PLP-DEs using quantitative, label-free mass spectrometry. Using these probes we accessed a significant portion of the Staphylococcus aureus PLP-DE proteome (73%) and annotate uncharacterized proteins as novel PLP-DEs. We also show that this approach can be used to study structural tolerance within PLP-DE active sites and to screen for off-targets of the PLP-DE inhibitor D-cycloserine.

PubMed: 30297752
DOI: 10.1038/s41557-018-0144-2

Experimental method

X-RAY DIFFRACTION (1.9 Å)