{"ymdb_id":"YMDB00284","created_at":"2011-05-29T18:02:01.000Z","updated_at":"2016-09-08T18:35:17.000Z","name":"D-Serine","cas":"312-84-5","state":"Solid","melting_point":"228 oC","description":"Serine (abbreviated as Ser or S) is an alpha-amino acid. The L-isomer is one of the 22 proteinogenic amino acids, i.e., the building blocks of proteins. D-isomers are used as carbon, nitrogen, and energy source.","experimental_water_solubility":"425 mg/mL at 25 oC [YALKOWSKY,SH \u0026 DANNENFELSER,RM (1992)]","experimental_logp_hydrophobicity":"-3.07 [HANSCH,C ET AL. (1995)]","location":null,"synthesis_reference":"Zhu, Yanxin; Yuan, Minglong; Yuan, Mingwei; Du, Bilin; Zheng, Ling.  Preparation of D-serine from acetylglycine.    Faming Zhuanli Shenqing Gongkai Shuomingshu  (2006),     4pp.","chebi_id":"16523","hmdb_id":"HMDB03406","kegg_id":"C00740","pubchem_id":"71077","cs_id":"64231","foodb_id":null,"wikipedia_link":"Serine","biocyc_id":"Serines","iupac":"(2R)-2-amino-3-hydroxypropanoic acid","traditional_iupac":"D-serine","logp":"-3.8877352328917727","pka":"15.166073878847005","alogps_solubility":"4.80e+02 g/l","alogps_logp":"-3.42","alogps_logs":"0.66","acceptor_count":"4","donor_count":"3","rotatable_bond_count":"2","polar_surface_area":"83.55000000000001","refractivity":"22.041000000000004","polarizability":"9.387821307652931","formal_charge":"0","physiological_charge":"0","pka_strongest_basic":"8.931303956589883","pka_strongest_acidic":"2.033990015469951","bioavailability":"1","number_of_rings":"0","rule_of_five":"1","ghose_filter":"0","veber_rule":"0","mddr_like_rule":"0","synonyms":["(2R)-2-amino-3-hydroxypropanoate","(2R)-2-amino-3-hydroxypropanoic acid","(R)-2-amino-3-hydroxypropanoate","(R)-2-amino-3-hydroxypropanoic acid","D-Serin","DL-Serine","DSN","Serine D-form"],"pathways":[{"name":"Glycine, serine and threonine metabolism","kegg_map_id":"00260"}],"growth_conditions":[],"references":[{"pubmed_id":21051339,"citation":"UniProt Consortium (2011). \"Ongoing and future developments at the Universal Protein Resource.\" Nucleic Acids Res 39:D214-D219."},{"pubmed_id":21062828,"citation":"Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). \"BRENDA, the enzyme information system in 2011.\" Nucleic Acids Res 39:D670-D676."},{"pubmed_id":15375647,"citation":"Yow, G. Y., Uo, T., Yoshimura, T., Esaki, N. (2004). \"D-amino acid N-acetyltransferase of Saccharomyces cerevisiae: a close homologue of histone acetyltransferase Hpa2p acting exclusively on free D-amino acids.\" Arch Microbiol 182:396-403."},{"pubmed_id":16246073,"citation":"Cowart, L. A., Hannun, Y. A. (2005). \"Using genomic and lipidomic strategies to investigate sphingolipid function in the yeast heat-stress response.\" Biochem Soc Trans 33:1166-1169."}],"proteins":[{"created_at":"2011-05-26T23:37:41.000Z","updated_at":"2011-05-29T14:08:02.000Z","name":"N-acetyltransferase HPA3","uniprot_id":"P39979","uniprot_name":"HPA3_YEAST","enzyme":true,"transporter":false,"gene_name":"HPA3","num_residues":179,"molecular_weight":"20698.5","theoretical_pi":"7.84","general_function":"Involved in N-acetyltransferase activity","specific_function":"N-acetyltransferase whose physiological acetyl acceptor substrate is still unknown. In vitro, histone acetylation is very weak","reactions":[{"id":2617,"direction":"\u003e","locations":"Cytoplasm. Nucleus","altext":"acetyl-CoA + a D-amino acid = CoA + an N-acetyl-D-amino acid","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":"Cytoplasm. Nucleus","genbank_gene_id":"U18795","genbank_protein_id":"603252","gene_card_id":"HPA3","chromosome_location":"chromosome 5","locus":"YEL066W","synonyms":[],"enzyme_classes":["2.3.1.-","2.3.1.36"],"go_classes":[{"category":"Component","description":" Not Available"},{"category":"Function","description":" catalytic activity"},{"category":"Function","description":" transferase activity"},{"category":"Function","description":" transferase activity, transferring acyl groups"},{"category":"Function","description":" transferase activity, transferring acyl groups other than amino-acyl groups"},{"category":"Function","description":" acyltransferase activity"},{"category":"Function","description":" acetyltransferase activity"},{"category":"Function","description":" N-acetyltransferase activity"},{"category":"Process","description":" metabolic process"}],"pfams":[{"name":"Acetyltransf_1","identifier":"PF00583"}],"pathways":[],"gene_sequence":"ATGAAAAAGACCCCAGACCCATCTCCACCTTTTGCAAGCACGAAGAACGTAGGCATGTCAAACGAAGAACCGGAAAAAATGGTTAACGATCGAATTGTGGTGAAGGCCATCGAGCCAAAAGATGAGGAAGCCTGGAACAAACTGTGGAAGGAGTATCAGGGTTTCCAAAAAACGGTTATGCCTCCGGAAGTAGCCACCACTACCTTCGCAAGGTTTATAGACCCTACGGTCAAACTATGGGGTGCTCTAGCCTTTGACACCGAGACCGGCGATGCAATTGGCTTTGCACACTACCTGAACCATTTGACGTCGTGGCATGTCGAAGAAGTTGTCTACATGAATGACTTATATGTCACTGAACGCGCAAGAGTCAAAGGCGTAGGTAGAAAGCTCATAGAATTTGTATACAGCCGTGCCGATGAGCTCGGTACGCCTGCAGTGTACTGGGTTACAGACCATTACAATCACCGCGCACAGTTGCTGTACACCAAAGTGGCTTACAAGACAGATAAGGTTCTTTACAAGAGAAACGGATACTGA","protein_sequence":"MKKTPDPSPPFASTKNVGMSNEEPEKMVNDRIVVKAIEPKDEEAWNKLWKEYQGFQKTVMPPEVATTTFARFIDPTVKLWGALAFDTETGDAIGFAHYLNHLTSWHVEEVVYMNDLYVTERARVKGVGRKLIEFVYSRADELGTPAVYWVTDHYNHRAQLLYTKVAYKTDKVLYKRNGY"},{"created_at":"2011-05-29T03:30:17.000Z","updated_at":"2011-05-29T05:06:53.000Z","name":"D-serine dehydratase","uniprot_id":"P53095","uniprot_name":"DSD1_YEAST","enzyme":true,"transporter":false,"gene_name":"DSD1","num_residues":428,"molecular_weight":"47827.39844","theoretical_pi":"7.64","general_function":"Involved in D-serine ammonia-lyase activity","specific_function":"Converts specifically D-serine to pyruvate and ammonia. May play a role in D-serine detoxification","reactions":[{"id":2838,"direction":"\u003e","locations":null,"altext":"D-serine = pyruvate + NH(3).","export":false,"pw_reaction_id":null,"source":null}],"signal_regions":"None","transmembrane_regions":"None","pdb_id":null,"cellular_location":null,"genbank_gene_id":null,"genbank_protein_id":null,"gene_card_id":"DSD1","chromosome_location":"chromosome 7","locus":"YGL196W","synonyms":["D-serine deaminase","DSD"],"enzyme_classes":["4.3.1.18"],"go_classes":[],"pfams":[{"name":"Ala_racemase_N","identifier":"PF01168"}],"pathways":[{"name":"Glycine, serine and threonine metabolism","kegg_map_id":"00260"}],"gene_sequence":"ATGAGCGATGTTCTATCTCAATATAAAGGGTGCTCAGTCAGAGATTTACCCACACCCAATTTCGTTATTAATGAAGAAAAATTTGATAAGAATTGTACGACAATGTTGAACAACGTTGAAAAGCTCAGCCAGGAATGTGGCGTACCAATCAAATTTCGTGCACACGTAAAAACGCATAAGACAGCAAAGGGAACTTTGAAACAATTGGGCCACGGACTTCCATTGGCTAAACGCACTACAAGAGCCATATTAGTATCAACTTTGAAAGAAGCAGAAGAACTTCTTAATTATCAAGATAGACAATGTTCGGATTATATTGACGATATAACATATAGTTTACCCTGTTGCGTTCCAGAGTTTATTCCTCTTTTGAGCAATTTGTCAAGAAGGGTGAATAATTTTCAGGTTTTTGTTGATAACATTGAACACTTGGAGAATTTAAAGAATTTCGGTAGGCCTGCTTCCGGCAAGAAATGGTCGGTTTTTATCAAGGTTGATATGGGGACTAAGAGGGCAGGTCTTGCTTTCGACTCTCCAGAATTTTTGAGTCTTTTAAAAAAACTGACTTCCTCAGAAATTAAAGAAGTAATTGAGCCATATGGGTTTTATGCTCATGCCGGACACAGCTACTCTTCAACCTCGATCAACGACACTCAGAATCTTTTGATGGAAGAAGTGAAAGCAGTCAATTCTGCCGCTAAAGTTTTGTGCTCTGTGGATCCTCAGTTTGATCCTTCTAAATTAACACTTTCTGTGGGCGCTACTCCGACTTCCAATTCTTTGAAACTCGATAATAAAAGTACCCTTGTTAAATTCATTACTACTCAATTAGTTAGTACGCTTGAAATCCACTGCGGTAATTACTGCATGTATGACCTGCAACAGGTGGCAACAGGCTGTGTCCAAGATCACGAATTGTCTGGTTTTGTATTAGGAACAGTACTATCATCTTACCCTTCTAGAGGTGAATTGTTGAGTAATACAGGTGTAATGTGTCTAACGCGAGAAGCATCCTCAATAAAAGGGTTTGGAATATGTGCTGATTTGGAACATGTGTTAAAATCCGAGAGTTTCAGTAGGGAATGGTATGTAGCAAGGGTCTCTCAAGAACACGGGATACTGAGGCCAATAAGAAACTGGAACGAAACTACTCCATTAAAATTAGGCAGCAAAATTGCCGTCCTTCCTCAACACGCTTGTATCACAATGGGACAATTTCCATATTATTTCGTGGTAAACAGCGAAGGCATTGTCAACGATGTTTGGTTACCTTTTCAGAAATGGTAA","protein_sequence":"MSDVLSQYKGCSVRDLPTPNFVINEEKFDKNCTTMLNNVEKLSQECGVPIKFRAHVKTHKTAKGTLKQLGHGLPLAKRTTRAILVSTLKEAEELLNYQDRQCSDYIDDITYSLPCCVPEFIPLLSNLSRRVNNFQVFVDNIEHLENLKNFGRPASGKKWSVFIKVDMGTKRAGLAFDSPEFLSLLKKLTSSEIKEVIEPYGFYAHAGHSYSSTSINDTQNLLMEEVKAVNSAAKVLCSVDPQFDPSKLTLSVGATPTSNSLKLDNKSTLVKFITTQLVSTLEIHCGNYCMYDLQQVATGCVQDHELSGFVLGTVLSSYPSRGELLSNTGVMCLTREASSIKGFGICADLEHVLKSESFSREWYVARVSQEHGILRPIRNWNETTPLKLGSKIAVLPQHACITMGQFPYYFVVNSEGIVNDVWLPFQKW"}]}