{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Nelson DL"],"funding":["American Heart Association","NCRR NIH HHS","National Institutes of Health"],"pagination":["13986-14002"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC5572919"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["292(34)"],"pubmed_abstract":["There is currently great interest in human serine racemase, the enzyme responsible for producing the NMDA co-agonist d-serine. Reported correlation of d-serine levels with disorders including Alzheimer's disease, ALS, and ischemic brain damage (elevated d-serine) and schizophrenia (reduced d-serine) has further piqued this interest. Reported here is a structure/activity relationship study of position Ser<sup>84</sup>, the putative <i>re</i>-face base. In the most extreme case of functional reprogramming, the S84D mutant displays a dramatic reversal of β-elimination substrate specificity in favor of l-serine over the normally preferred l-serine-<i>O</i>-sulfate (∼1200-fold change in <i>k</i><sub>cat</sub>/<i>K<sub>m</sub></i> ratios) and l (l-THA; ∼5000-fold change in <i>k</i><sub>cat</sub>/<i>K<sub>m</sub></i> ratios) alternative substrates. On the other hand, the S84T (which performs l-Ser racemization activity), S84A (good <i>k</i><sub>cat</sub> but high <i>K<sub>m</sub></i> for l-THA elimination), and S84N mutants (nearly WT efficiency for l-Ser elimination) displayed intermediate activity, all showing a preference for the anionic substrates, but generally attenuated compared with the native enzyme. Inhibition studies with l-<i>erythro</i>-β-hydroxyaspartate follow this trend, with both WT serine racemase and the S84N mutant being competitively inhibited, with <i>K<sub>i</sub></i> = 31 ± 1.5 μm and 1.5 ± 0.1 mm, respectively, and the S84D being inert to inhibition. Computational modeling pointed to a key role for residue Arg-135 in binding and properly positioning the l-THA and l-serine-<i>O</i>-sulfate substrates and the l-<i>erythro</i>-β-hydroxyaspartate inhibitor. Examination of available sequence data suggests that Arg-135 may have originated for l-THA-like β-elimination function in earlier evolutionary variants, and examination of available structural data suggests that a Ser<sup>84</sup>-H<sub>2</sub>O-Lys<sup>114</sup> hydrogen-bonding network in human serine racemase lowers the p<i>K<sub>a</sub></i> of the Ser<sup>84</sup><i>re</i>-face base."],"journal":["The Journal of biological chemistry"],"pubmed_title":["Human serine racemase structure/activity relationship studies provide mechanistic insight and point to position 84 as a hot spot for β-elimination function."],"pmcid":["PMC5572919"],"funding_grant_id":["16GRNT313400012","RR016544","C06 RR016544"],"pubmed_authors":["Graham DL","Nelson DL","Berkowitz DB","Beio ML","Applegate GA"],"additional_accession":[]},"is_claimable":false,"name":"Human serine racemase structure/activity relationship studies provide mechanistic insight and point to position 84 as a hot spot for β-elimination function.","description":"There is currently great interest in human serine racemase, the enzyme responsible for producing the NMDA co-agonist d-serine. Reported correlation of d-serine levels with disorders including Alzheimer's disease, ALS, and ischemic brain damage (elevated d-serine) and schizophrenia (reduced d-serine) has further piqued this interest. Reported here is a structure/activity relationship study of position Ser<sup>84</sup>, the putative <i>re</i>-face base. In the most extreme case of functional reprogramming, the S84D mutant displays a dramatic reversal of β-elimination substrate specificity in favor of l-serine over the normally preferred l-serine-<i>O</i>-sulfate (∼1200-fold change in <i>k</i><sub>cat</sub>/<i>K<sub>m</sub></i> ratios) and l (l-THA; ∼5000-fold change in <i>k</i><sub>cat</sub>/<i>K<sub>m</sub></i> ratios) alternative substrates. On the other hand, the S84T (which performs l-Ser racemization activity), S84A (good <i>k</i><sub>cat</sub> but high <i>K<sub>m</sub></i> for l-THA elimination), and S84N mutants (nearly WT efficiency for l-Ser elimination) displayed intermediate activity, all showing a preference for the anionic substrates, but generally attenuated compared with the native enzyme. Inhibition studies with l-<i>erythro</i>-β-hydroxyaspartate follow this trend, with both WT serine racemase and the S84N mutant being competitively inhibited, with <i>K<sub>i</sub></i> = 31 ± 1.5 μm and 1.5 ± 0.1 mm, respectively, and the S84D being inert to inhibition. Computational modeling pointed to a key role for residue Arg-135 in binding and properly positioning the l-THA and l-serine-<i>O</i>-sulfate substrates and the l-<i>erythro</i>-β-hydroxyaspartate inhibitor. Examination of available sequence data suggests that Arg-135 may have originated for l-THA-like β-elimination function in earlier evolutionary variants, and examination of available structural data suggests that a Ser<sup>84</sup>-H<sub>2</sub>O-Lys<sup>114</sup> hydrogen-bonding network in human serine racemase lowers the p<i>K<sub>a</sub></i> of the Ser<sup>84</sup><i>re</i>-face base.","dates":{"release":"2017-01-01T00:00:00Z","publication":"2017 Aug","modification":"2025-04-26T01:24:15.321Z","creation":"2019-03-26T23:52:10Z"},"accession":"S-EPMC5572919","cross_references":{"pubmed":["28696262"],"doi":["10.1074/jbc.m117.777904","10.1074/jbc.M117.777904"]}}