Aspartate racemase
| aspartate racemase | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
ExPASy | NiceZyme view | ||||||||
| KEGG | KEGG entry | ||||||||
| MetaCyc | metabolic pathway | ||||||||
| PRIAM | profile | ||||||||
| PDB structures | RCSB PDB PDBe PDBsum | ||||||||
| Gene Ontology | AmiGO / QuickGO | ||||||||
| |||||||||
In
- L-aspartate D-aspartate
This enzyme belongs to the family of
The systematic name of this enzyme class is aspartate racemase. Other names in common use include D-aspartate racemase, and McyF.[1]
Discovery
Aspartate racemase was first discovered in the gram-positive bacteria Streptococcus faecalis by Lamont et al. in 1972.[2] It was then determined that aspartate racemase also racemizes L-alanine around half as quickly as it does L-aspartate, but does not show racemase activity in the presence of L-glutamate.
Structure
The crystallographic structure of bacterial aspartate racemase has been solved in Pyrococcus horikoshii OT3,[3] Escherichia coli, Microcystis aeruginosa, and Picrophilus torridus DSM 9790.
Homodimer
In most bacteria for which the structure is known, aspartate racemase exists as a
Two highly conserved
In E. coli, one of the active cysteine residues is substituted for a threonine residue, allowing for much greater substrate promiscuity.[5] Notably, aspartate racemase in E. coli is also able to catalyze the racemization of glutamate.
Monomer
In 2004, an aspartate racemase was discovered in Bifidobacterium bifidum as a 27 kDa monomer.[6] This protein shares nearly identical enzymological properties with homodimeric aspartate racemase isolated from Streptococcus thermophilus, but has the added characteristic that its thermal stability increases significantly in the presence of aspartate.
Reaction mechanism
Aspartate racemase catalyzes the following reaction:
Aspartate racemase can accept either L-aspartate or D-aspartate as substrates.
Amino acid racemization is carried out by two dominant mechanisms: one-base mechanisms and two-base mechanisms.[7] In one-base mechanisms, a proton acceptor abstracts the α-hydrogen from the substrate amino acid to form a carbanion intermediate until reprotonated at the other face of the α-carbon. Racemases dependent on pyridoxal-5-phosphate (PLP) typically leverage one-base mechanisms. In the two-base mechanism, an alpha hydrogen is abstracted by a base on one face of the amino acid while another protonated base concertedly donates its hydrogen onto the other face of the amino acid.
PLP-independent mechanism
Aspartate racemases in bacteria function in the absence of PLP, suggesting a PLP-independent mechanism.[5] A two-base mechanism is supported in the literature, carried out by two thiol groups:
Other PLP-independent isomerases in bacteria include glutamate racemase, proline racemase, and hydroxyproline-2-epimerase.
PLP-dependent mechanism
Mammalian aspartate racemase, in contrast with bacterial aspartate racemase, is a PLP-dependent enzyme. The exact mechanism is unknown, but it is hypothesized to proceed similarly to mammalian serine racemase as below:
Inhibition
General inhibitors for cysteine residues have shown to be effective agents against monomeric aspartate racemase.[2][5] N-ethylmaleimide and 5,5'-dithiobis(2-nitrobenzoate) both inhibit monomeric aspartate racemase at 1mM.
Function
Metabolism of D-aspartate
One of the primary functions of aspartate racemase in bacteria is the metabolism of D-aspartate.[8][9] The beginning of D-aspartate metabolism is its conversion to L-alanine. First, D-aspartate is isomerized to L-aspartate by aspartate racemase, followed by decarboxylation to form L-alanine.[9]
Peptidoglycan synthesis
D-amino acids are common within the peptidoglycan of bacteria.[10] In Bifidobacterium bifidum, D-aspartate is formed from L-aspartate via aspartate racemase and used as a cross-linker moiety in the peptidoglycan.[6]
Mammalian neurogenesis
Aspartate racemase is highly expressed in the brain, the heart, and the testes of mammals, all tissues in which D-aspartate is present.
