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Protein

Serine racemase

Gene

SRR

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the synthesis of D-serine from L-serine. D-serine is a key coagonist with glutamate at NMDA receptors. Has dehydratase activity towards both L-serine and D-serine.2 Publications

Catalytic activityi

L-serine = D-serine.1 Publication
L-serine = pyruvate + NH3.1 Publication
D-serine = pyruvate + NH3.1 Publication

Cofactori

pyridoxal 5'-phosphate1 Publication

Enzyme regulationi

Allosterically activated by magnesium, and possibly also other divalent metal cations. Allosterically activated by ATP, ADP or GTP. Competitively inhibited by malonate.

Kineticsi

  1. KM=6.5 mM for L-serine1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei51 – 511ATPBy similarity
    Active sitei56 – 561Proton acceptorBy similarity
    Active sitei84 – 841Proton acceptorBy similarity
    Binding sitei121 – 1211ATPBy similarity
    Binding sitei135 – 1351SubstrateCurated
    Metal bindingi210 – 2101Magnesium
    Metal bindingi214 – 2141Magnesium; via carbonyl oxygen
    Metal bindingi216 – 2161Magnesium

    GO - Molecular functioni

    • ATP binding Source: UniProtKB
    • calcium ion binding Source: UniProtKB
    • D-serine ammonia-lyase activity Source: GO_Central
    • glycine binding Source: UniProtKB
    • L-serine ammonia-lyase activity Source: UniProtKB
    • magnesium ion binding Source: UniProtKB
    • PDZ domain binding Source: UniProtKB
    • protein homodimerization activity Source: UniProtKB
    • pyridoxal phosphate binding Source: UniProtKB
    • serine racemase activity Source: UniProtKB
    • threonine racemase activity Source: UniProtKB

    GO - Biological processi

    • aging Source: Ensembl
    • brain development Source: GO_Central
    • D-serine biosynthetic process Source: UniProtKB
    • D-serine metabolic process Source: UniProtKB
    • L-serine metabolic process Source: UniProtKB
    • protein homotetramerization Source: UniProtKB
    • pyruvate biosynthetic process Source: UniProtKB
    • response to drug Source: Ensembl
    • response to lipopolysaccharide Source: UniProtKB
    • response to morphine Source: Ensembl
    • serine family amino acid metabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase, Lyase

    Keywords - Ligandi

    ATP-binding, Magnesium, Metal-binding, Nucleotide-binding, Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciMetaCyc:HS09614-MONOMER.
    BRENDAi5.1.1.18. 2681.
    SignaLinkiQ9GZT4.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Serine racemase (EC:4.3.1.17, EC:4.3.1.18, EC:5.1.1.18)
    Alternative name(s):
    D-serine ammonia-lyase
    D-serine dehydratase
    L-serine ammonia-lyase
    L-serine dehydratase
    Gene namesi
    Name:SRR
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640 Componenti: Chromosome 17

    Organism-specific databases

    HGNCiHGNC:14398. SRR.

    Subcellular locationi

    GO - Cellular componenti

    • apical part of cell Source: Ensembl
    • cytoplasm Source: UniProtKB
    • neuronal cell body Source: UniProtKB
    • plasma membrane Source: Ensembl
    Complete GO annotation...

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA37877.

    Chemistry

    DrugBankiDB00133. L-Serine.

    Polymorphism and mutation databases

    BioMutaiSRR.
    DMDMi20139924.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 340340Serine racemasePRO_0000185650Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei56 – 561N6-(pyridoxal phosphate)lysine
    Modified residuei113 – 1131S-nitrosocysteineBy similarity

    Post-translational modificationi

    S-nitrosylated, leading to decrease the enzyme activity.By similarity

    Keywords - PTMi

    S-nitrosylation

    Proteomic databases

    MaxQBiQ9GZT4.
    PaxDbiQ9GZT4.
    PRIDEiQ9GZT4.

    PTM databases

    PhosphoSiteiQ9GZT4.

    Expressioni

    Tissue specificityi

    Brain: expressed at high levels in hippocampus and corpus callosum, intermediate levels in substantia nigra and caudate, and low levels in amygdala, thalamus, and subthalamic nuclei. Expressed in heart, skeletal muscle, kidney and liver.1 Publication

    Gene expression databases

    BgeeiQ9GZT4.
    CleanExiHS_SRR.
    ExpressionAtlasiQ9GZT4. baseline and differential.
    GenevisibleiQ9GZT4. HS.

    Organism-specific databases

    HPAiCAB015343.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    BioGridi121963. 6 interactions.
    IntActiQ9GZT4. 1 interaction.
    STRINGi9606.ENSP00000339435.

    Structurei

    Secondary structure

    1
    340
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi9 – 1911Combined sources
    Helixi20 – 223Combined sources
    Helixi32 – 387Combined sources
    Beta strandi40 – 467Combined sources
    Helixi47 – 493Combined sources
    Helixi51 – 533Combined sources
    Helixi56 – 6510Combined sources
    Beta strandi79 – 824Combined sources
    Helixi86 – 9712Combined sources
    Beta strandi102 – 1076Combined sources
    Helixi112 – 1209Combined sources
    Beta strandi124 – 1285Combined sources
    Helixi132 – 14615Combined sources
    Beta strandi153 – 1553Combined sources
    Helixi157 – 17317Combined sources
    Beta strandi179 – 1835Combined sources
    Beta strandi185 – 1873Combined sources
    Helixi188 – 20013Combined sources
    Beta strandi204 – 2118Combined sources
    Helixi212 – 2143Combined sources
    Helixi216 – 2238Combined sources
    Helixi238 – 2403Combined sources
    Helixi248 – 2558Combined sources
    Beta strandi258 – 2625Combined sources
    Helixi264 – 27815Combined sources
    Helixi284 – 29411Combined sources
    Helixi296 – 3005Combined sources
    Beta strandi307 – 3126Combined sources
    Helixi321 – 3233Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3L6BX-ray1.50A1-340[»]
    3L6RX-ray1.70A1-340[»]
    ProteinModelPortaliQ9GZT4.
    SMRiQ9GZT4. Positions 3-329.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9GZT4.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni238 – 2392Substrate bindingBy similarity

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG1171.
    GeneTreeiENSGT00550000075026.
    HOGENOMiHOG000046974.
    HOVERGENiHBG023167.
    InParanoidiQ9GZT4.
    KOiK12235.
    OMAiDTPKTIA.
    OrthoDBiEOG7HB5B2.
    PhylomeDBiQ9GZT4.
    TreeFamiTF313346.

    Family and domain databases

    InterProiIPR000634. Ser/Thr_deHydtase_PyrdxlP-BS.
    IPR001926. TrpB-like_PLP-dep.
    [Graphical view]
    PfamiPF00291. PALP. 1 hit.
    [Graphical view]
    SUPFAMiSSF53686. SSF53686. 1 hit.
    PROSITEiPS00165. DEHYDRATASE_SER_THR. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9GZT4-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MCAQYCISFA DVEKAHINIR DSIHLTPVLT SSILNQLTGR NLFFKCELFQ
    60 70 80 90 100
    KTGSFKIRGA LNAVRSLVPD ALERKPKAVV THSSGNHGQA LTYAAKLEGI
    110 120 130 140 150
    PAYIVVPQTA PDCKKLAIQA YGASIVYCEP SDESRENVAK RVTEETEGIM
    160 170 180 190 200
    VHPNQEPAVI AGQGTIALEV LNQVPLVDAL VVPVGGGGML AGIAITVKAL
    210 220 230 240 250
    KPSVKVYAAE PSNADDCYQS KLKGKLMPNL YPPETIADGV KSSIGLNTWP
    260 270 280 290 300
    IIRDLVDDIF TVTEDEIKCA TQLVWERMKL LIEPTAGVGV AAVLSQHFQT
    310 320 330 340
    VSPEVKNICI VLSGGNVDLT SSITWVKQAE RPASYQSVSV
    Length:340
    Mass (Da):36,566
    Last modified:March 1, 2001 - v1
    Checksum:i873342C62D5D7B9D
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF169974 mRNA. Translation: AAG27081.1.
    AY034081 mRNA. Translation: AAK58495.1.
    AK023169 mRNA. Translation: BAB14442.1.
    CR457300 mRNA. Translation: CAG33581.1.
    CH471108 Genomic DNA. Translation: EAW90553.1.
    CH471108 Genomic DNA. Translation: EAW90554.1.
    CH471108 Genomic DNA. Translation: EAW90555.1.
    BC074728 mRNA. Translation: AAH74728.1.
    CCDSiCCDS11017.1.
    RefSeqiNP_068766.1. NM_021947.2.
    XP_006721628.1. XM_006721565.2.
    XP_006721629.1. XM_006721566.2.
    XP_011522276.1. XM_011523974.1.
    UniGeneiHs.461954.

    Genome annotation databases

    EnsembliENST00000344595; ENSP00000339435; ENSG00000167720.
    GeneIDi63826.
    KEGGihsa:63826.
    UCSCiuc002fue.1. human.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF169974 mRNA. Translation: AAG27081.1.
    AY034081 mRNA. Translation: AAK58495.1.
    AK023169 mRNA. Translation: BAB14442.1.
    CR457300 mRNA. Translation: CAG33581.1.
    CH471108 Genomic DNA. Translation: EAW90553.1.
    CH471108 Genomic DNA. Translation: EAW90554.1.
    CH471108 Genomic DNA. Translation: EAW90555.1.
    BC074728 mRNA. Translation: AAH74728.1.
    CCDSiCCDS11017.1.
    RefSeqiNP_068766.1. NM_021947.2.
    XP_006721628.1. XM_006721565.2.
    XP_006721629.1. XM_006721566.2.
    XP_011522276.1. XM_011523974.1.
    UniGeneiHs.461954.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3L6BX-ray1.50A1-340[»]
    3L6RX-ray1.70A1-340[»]
    ProteinModelPortaliQ9GZT4.
    SMRiQ9GZT4. Positions 3-329.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi121963. 6 interactions.
    IntActiQ9GZT4. 1 interaction.
    STRINGi9606.ENSP00000339435.

    Chemistry

    BindingDBiQ9GZT4.
    ChEMBLiCHEMBL4460.
    DrugBankiDB00133. L-Serine.

    PTM databases

    PhosphoSiteiQ9GZT4.

    Polymorphism and mutation databases

    BioMutaiSRR.
    DMDMi20139924.

    Proteomic databases

    MaxQBiQ9GZT4.
    PaxDbiQ9GZT4.
    PRIDEiQ9GZT4.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENST00000344595; ENSP00000339435; ENSG00000167720.
    GeneIDi63826.
    KEGGihsa:63826.
    UCSCiuc002fue.1. human.

    Organism-specific databases

    CTDi63826.
    GeneCardsiGC17P002212.
    HGNCiHGNC:14398. SRR.
    HPAiCAB015343.
    MIMi606477. gene.
    neXtProtiNX_Q9GZT4.
    PharmGKBiPA37877.
    GenAtlasiSearch...

    Phylogenomic databases

    eggNOGiCOG1171.
    GeneTreeiENSGT00550000075026.
    HOGENOMiHOG000046974.
    HOVERGENiHBG023167.
    InParanoidiQ9GZT4.
    KOiK12235.
    OMAiDTPKTIA.
    OrthoDBiEOG7HB5B2.
    PhylomeDBiQ9GZT4.
    TreeFamiTF313346.

    Enzyme and pathway databases

    BioCyciMetaCyc:HS09614-MONOMER.
    BRENDAi5.1.1.18. 2681.
    SignaLinkiQ9GZT4.

    Miscellaneous databases

    ChiTaRSiSRR. human.
    EvolutionaryTraceiQ9GZT4.
    GeneWikiiSerine_racemase.
    GenomeRNAii63826.
    NextBioi65538.
    PROiQ9GZT4.
    SOURCEiSearch...

    Gene expression databases

    BgeeiQ9GZT4.
    CleanExiHS_SRR.
    ExpressionAtlasiQ9GZT4. baseline and differential.
    GenevisibleiQ9GZT4. HS.

    Family and domain databases

    InterProiIPR000634. Ser/Thr_deHydtase_PyrdxlP-BS.
    IPR001926. TrpB-like_PLP-dep.
    [Graphical view]
    PfamiPF00291. PALP. 1 hit.
    [Graphical view]
    SUPFAMiSSF53686. SSF53686. 1 hit.
    PROSITEiPS00165. DEHYDRATASE_SER_THR. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Human serine racemase: molecular cloning, genomic organization and functional expression."
      De Miranda J., Santoro A., Engelender S., Wolosker H.
      Gene 256:183-188(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION.
      Tissue: Brain.
    2. Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
    3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    4. "Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
      Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
      Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    6. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Brain.
    7. Lubec G., Chen W.-Q., Sun Y.
      Submitted (DEC-2008) to UniProtKB
      Cited for: PROTEIN SEQUENCE OF 97-114; 116-135; 206-221 AND 226-241, IDENTIFICATION BY MASS SPECTROMETRY.
      Tissue: Fetal brain cortex.
    8. "The structure of mammalian serine racemase: evidence for conformational changes upon inhibitor binding."
      Smith M.A., Mack V., Ebneth A., Moraes I., Felicetti B., Wood M., Schonfeld D., Mather O., Cesura A., Barker J.
      J. Biol. Chem. 285:12873-12881(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 3-340 IN COMPLEX WITH MANGANESE IONS; MALONATE AND PYRIDOXAL PHOSPHATE, COFACTOR, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.

    Entry informationi

    Entry nameiSRR_HUMAN
    AccessioniPrimary (citable) accession number: Q9GZT4
    Secondary accession number(s): D3DTI5, Q6IA55
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 31, 2002
    Last sequence update: March 1, 2001
    Last modified: July 22, 2015
    This is version 118 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Allosteric enzyme, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Human chromosome 17
      Human chromosome 17: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.