The Structure of Mammalian Serine Racemase

Abstract

Serine racemase is responsible for the synthesis of D-serine, an endogenous co-agonist for N-methyl-D-aspartate receptor-type glutamate receptors (NMDARs). This pyridoxal 5-phosphatedependent enzyme is involved both in the reversible conversion of L-to D-serine and serine catabolism by ␣,␤-elimination of water, thereby regulating D-serine levels. Because D-serine affects NMDAR signaling throughout the brain, serine racemase is a promising target for the treatment of disorders related to NMDAR dysfunction. To provide a molecular basis for rational drug design the x-ray crystal structures of human and rat serine racemase were determined at 1.5-and 2.1-Å resolution, respectively, and in the presence and absence of the orthosteric inhibitor malonate. The structures revealed a fold typical of ␤-family pyridoxal 5-phosphate enzymes, with both a large domain and a flexible small domain associated into a symmetric dimer, and indicated a ligand-induced rearrangement of the small domain that organizes the active site for specific turnover of the substrate.N-Methyl-D-aspartate receptor-type glutamate receptors (NMDARs) 2 are a key component in glutamatergic transmission implicated in the development, function, and plasticity of the nervous system. In addition to the neurotransmitter glutamate, the activation of NMDARs requires the binding of either of the two endogenous co-agonists, glycine or D-serine, to the NMDAR "glycine modulatory site" (1, 2). Although both amino acids have similar potency as co-agonists, they display regional differences in modulating NMDAR function (3, 4). According to its distribution within the CNS, D-serine exerts its function predominantly in corticolimbic brain structures (5). This pivotal role of D-serine is supported by several experimental findings, including depletion studies in neuronal tissue preparations, indicating a strong reduction in NMDAR-mediated transmission and impaired synaptic plasticity in the absence of D-serine (6, 7).D-serine is produced by enzymatic conversion of L-to D-serine mediated by the pyridoxal 5Ј-phosphate (PLP)-containing enzyme serine racemase (SR). Mammalian SR was first purified from rat brain and functionally characterized in 1999 by Wolosker and colleagues (8). The enzyme is expressed in glial cells and neurons and constitutes the sole endogenous source for D-serine in mammals (9). Both human and rodent SR have been purified and extensively studied to generate comprehensive knowledge of the enzymatic characteristics and allosteric modulation by a number of agents such as ATP and Mg 2ϩ ions. In addition to serine isomerization, the enzyme catalyzes the ␣,␤-elimination of water from L-and D-serine to produce pyruvate and ammonia, thus, offering the possibility for SR not only to elevate but also to reduce the level of D-serine (5), a role that previously has mainly been attributed to D-amino acid oxidase (10).Recent data from SR-deficient mice strongly implicate this enzyme in the process of NMDAR-dependent plasticity and neurotoxicity. Knock-out mice were ...

Addressing the Conformational Flexibility of Serine Racemase by Combining Targeted Molecular Dynamics, Conformational Sampling and Docking Studies

“…[7] The open-closed transition was simulated in the presence of either the physiological substrate L-Ser (2) or the orthosteric inhibitor malonate (3). Thus, the X-ray structures of malonate bound to hSR [7] (pdb code 3L6B) and to the holo rat SR (rSR) [7] (pdb code 3HMK) were selected as representative of a full close and full open conformations, respectively.…”

“…Modifided SR with PDD (lysino-d-alanyl residue) without any orthosteric/allosteric ligands 2ZR8 [29] Schizosaccharomyces pombe Modifided SR with PDD (lysino-d-alanyl residue) complexed with serine 3HMK [7] Rattus norvegicus Without any orthosteric/allosteric ligands 3L6C [7] …”

“…First, we intended to shed light on the molecular mechanism of the enzyme closure by identifying key residues responsible for the conformational movements. Second, we used the targeted trajectory between the open [7] Homo sapiens Complexed with malonate 3L6R [7] Homo sapiens…”

“…[7,31] This is particularly important for structure based drug design, [32][33][34] since the choice of a specific enzyme conformation may bias toward a subset of features or limited ligand size, thus neglecting other potentially relevant information.…”

“…Mammalian SR adopts the expected fold of b-family PLP-dependent enzymes, with a large domain, and a small, flexible domain which rearrange upon substrate binding to shape the active site, thus allowing L-Ser processing. [7][8][9] The orthosteric inhibitor malonate binds the active site thus promoting the conformational changes towards a closed conformation and eventually hampering the entry of the substrate (Figure 1). …”