Human Serine Racemase: Key Residues/Active Site Motifs and Their Relation to Enzyme Function

Abstract

Serine racemase (SR) is the first racemase enzyme to be identified in human biology and converts L-serine to D-serine, an important neuronal signaling molecule that serves as a co-agonist of the NMDA (N-methyl-D-aspartate) receptor. This overview describes key molecular features of the enzyme, focusing on the side chains and binding motifs that control PLP (pyridoxal phosphate) cofactor binding as well as activity modulation through the binding of both divalent cations and ATP, the latter showing allosteric modulation. Discussed are catalytically important residues in the active site including K56 and S84—the si- and re-face bases, respectively,—and R135, a residue that appears to play a critical role in the binding of both negatively charged alternative substrates and inhibitors. The interesting bifurcated mechanism followed by this enzyme whereby substrate L-serine can be channeled either into D-serine (racemization pathway) or into pyruvate (β-elimination pathway) is discussed extensively, as are studies that focus on a key loop region (the so-called “triple serine loop”), the modification of which can be used to invert the normal in vitro preference of this enzyme for the latter pathway over the former. The possible cross-talk between the PLP enzymes hSR and hCBS (human cystathionine β-synthase) is discussed, as the former produces D-serine and the latter produces H2S, both of which stimulate the NMDAR and both of which have been implicated in neuronal infarction pursuant to ischemic stroke. Efforts to gain a more complete mechanistic understanding of these PLP enzymes are expected to provide valuable insights for the development of specific small molecule modulators of these enzymes as tools to study their roles in neuronal signaling and in modulation of NMDAR function.

d-amino Acids in Health and Disease: A Focus on Cancer

“…Furthermore, the results of a recent rodent study indicate that serine racemase might also be involved in the biosynthesis of d -Asp [70]. Additionally, serine racemase also catalyzes the alpha,beta-elimination of water from both l -Ser and d -Ser, resulting in the production of pyruvate and ammonia [22,71].…”

Tyrosine 121 moves revealing a druggable pocket that couples catalysis to ATP-binding in serine racemase

“…SR activity is dependent on the presence of divalent metal ions. It has been reported that rat brain SR is activated in the presence of Mn 2+ ions (153% at 10 μM), Ca 2+ ions (134% at 1 mM) and Mg 2+ ions (112% at 10 μM) 12,41 . The original crystal structure of hSR with malonate, 3L6B 30 contains Mn 2+ ions, while our new structure with ATP and malonate (6ZSP) contains Mg 2+ ions, and our new 1.8 Å holoenzyme structure (6ZUJ) contains Ca 2+ in the metal binding centre (Fig.…”

“…In addition to the racemisation of D- and L-serine (Fig. 1a-c), SR can also act as a dehydratase 12 , catalysing the β-elimination of the side-chain hydroxyl of serine. The β-elimination produces aminoacrylate/iminoproprionate 13,14 , two interchangeable tautomers 15 , which are unstable in aqueous solution where they are hydrolysed into pyruvate and ammonia (Fig.…”

“…Both the racemisation and elimination reactions of SR are activated to some degree by ATP, but not identically in mammals and yeast. The activating effect of ATP can be potentiated by the divalent cations Mg 2+ , Mn 2+ , and Ca 2+ 12,39–41 . The cation-nucleotide complex (e.g.…”

Racemases and epimerases operating through a 1,1-proton transfer mechanism: reactivity, mechanism and inhibition

“…Several PLP-dependent racemases catalyse elimination reactions. [129][130][131][132][133] The classic example is alanine racemase (Scheme 3) which b-eliminates halogens from 3-fluoroalanine 12 and 3-chloroalanine 13. 132 O-Carbamoyl-R-serine 14R and O-acetyl-R-serine 15R act as irreversible inhibitors whilst O-carbamoyl-S-serine 14S and O-acetyl-S-serine 15S are reversible competitive inhibitors.…”