Structural basis for redox sensitivity in Corynebacterium glutamicum diaminopimelate epimerase: an enzyme involved in l-lysine biosynthesis

Abstract

Diaminopimelate epimerase (DapF) is one of the crucial enzymes involved in l-lysine biosynthesis, where it converts l,l-diaminopimelate (l,l-DAP) into d,l-DAP. DapF is also considered as an attractive target for the development of antibacterial drugs. Here, we report the crystal structure of DapF from Corynebacterium glutamicum (CgDapF). Structures of CgDapF obtained under both oxidized and reduced conditions reveal that the function of CgDapF is regulated by redox-switch modulation via reversible disulfide bond formation between two catalytic cysteine residues. Under oxidized condition, two catalytic cysteine residues form a disulfide bond; these same cysteine residues exist in reduced form under reduced condition. Disulfide bond formation also induces a subsequent structural change in the dynamic catalytic loop at the active site, which results in open/closed conformational change at the active site. We also determined the crystal structure of CgDapF in complex with its product d,l-DAP, and elucidated how the enzyme recognizes its substrate l,l-DAP as a substrate. Moreover, the structure in complex with the d,l-DAP product reveals that CgDapF undergoes a large open/closed domain movement upon substrate binding, resulting in a completely buried active site with the substrate bound.

Nutty-like flavor production by Corynbacterium glutamicum 1220T from enzymatic soybean hydrolysate. Effect of encapsulation and storage on the nutty flavoring quality

“…Biotechnological use of C. glutamicum has been impressive progress for the production of various chemicals [8] . Considerable quantity of alkypyrazines had been produced by C. glutamicum with trimethylpyrazine (TMP), TTMP and acetoin as main compounds [9] .…”

Elucidation of the d‐lysine biosynthetic pathway in the hyperthermophile Thermotoga maritima

“…Unexpectedly, our findings show that the quaternary structure of TM1522 may be trimeric (Fig. B), whereas Dpm epimerases from E. coli (PDB ID: http://www.rcsb.org/pdb/search/structidSearch.do?structureId=4IJZ) , Bacillus anthracis (PDB ID: http://www.rcsb.org/pdb/search/structidSearch.do?structureId=2OTN), and Corynebacterium glutamicum (PDB ID: http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5H2G, http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5H2Y, and http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5M47) are dimeric and the Haemophilus influenzae orthology (PDB ID: http://www.rcsb.org/pdb/search/structidSearch.do?structureId=1BWZ) is monomeric .…”

“…Unexpectedly, our findings show that the quaternary structure of TM1522 may be trimeric (Fig. 2B), whereas Dpm epimerases from E. coli (PDB ID: 4IJZ) [54], Bacillus anthracis (PDB ID: 2OTN), and Corynebacterium glutamicum (PDB ID: 5H2G, 5H2Y, and 5M47) are dimeric [55] and the Haemophilus influenzae orthology (PDB ID: 1BWZ) is monomeric [56].…”

Overexpression of thermostable meso-diaminopimelate dehydrogenase to redirect diaminopimelate pathway for increasing L-lysine production in Escherichia coli

“…L-lysine, one of the essential amino acids for animals and humans 1 , is widely used in feed, food, and pharmaceutical industry, etc . The global marketplace for L-lysine is expected to amount to $6.96 billion by 2020 as consumption increases 2,3 . In industry, L-lysine is mainly produced by microbial fermentation employing mutant strains of bacteria, such as Corynebacterium sp.…”