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Protein

Serine racemase

Gene

Srr

Organism
Rattus norvegicus (Rat)
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 (By similarity). Competitively inhibited by malonate.By similarity1 Publication

Kineticsi

  1. KM=3.7 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 – 2101MagnesiumBy similarity
    Metal bindingi214 – 2141Magnesium; via carbonyl oxygen
    Metal bindingi216 – 2161MagnesiumBy similarity

    GO - Molecular functioni

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

    GO - Biological processi

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

    Keywords - Molecular functioni

    Isomerase, Lyase

    Keywords - Ligandi

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

    Enzyme and pathway databases

    BRENDAi5.1.1.18. 5301.

    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
    OrganismiRattus norvegicus (Rat)
    Taxonomic identifieri10116 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
    ProteomesiUP000002494 Componenti: Chromosome 10

    Organism-specific databases

    RGDi735094. Srr.

    Subcellular locationi

    GO - Cellular componenti

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

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 333333Serine racemasePRO_0000286173Add
    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

    PaxDbiQ76EQ0.
    PRIDEiQ76EQ0.

    PTM databases

    PhosphoSiteiQ76EQ0.

    Expressioni

    Gene expression databases

    GenevestigatoriQ76EQ0.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    BioGridi257487. 1 interaction.
    STRINGi10116.ENSRNOP00000050774.

    Structurei

    Secondary structure

    1
    333
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi9 – 1911Combined sources
    Turni20 – 223Combined sources
    Helixi32 – 387Combined sources
    Beta strandi40 – 467Combined sources
    Helixi47 – 493Combined sources
    Helixi51 – 533Combined sources
    Helixi57 – 6610Combined sources
    Beta strandi70 – 734Combined sources
    Beta strandi79 – 824Combined sources
    Helixi86 – 9712Combined sources
    Beta strandi102 – 1076Combined sources
    Helixi112 – 1209Combined sources
    Beta strandi124 – 1285Combined sources
    Helixi134 – 14613Combined sources
    Beta strandi153 – 1553Combined sources
    Helixi157 – 1637Combined sources
    Helixi165 – 1739Combined 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
    Turni246 – 2483Combined sources
    Helixi249 – 2557Combined sources
    Beta strandi258 – 2625Combined sources
    Helixi264 – 27815Combined sources
    Helixi284 – 29411Combined sources
    Helixi296 – 3005Combined sources
    Beta strandi307 – 3126Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3HMKX-ray2.10A/B1-333[»]
    3L6CX-ray2.20A/B1-333[»]
    ProteinModelPortaliQ76EQ0.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ76EQ0.

    Family & Domainsi

    Region

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

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG1171.
    GeneTreeiENSGT00550000075026.
    HOGENOMiHOG000046974.
    HOVERGENiHBG023167.
    InParanoidiQ76EQ0.
    KOiK12235.
    OMAiWKEEYLT.
    OrthoDBiEOG7HB5B2.
    PhylomeDBiQ76EQ0.
    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.

    Q76EQ0-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MCAQYCISFA DVEKAHLNIQ DSVHLTPVLT SSILNQIAGR NLFFKCELFQ
    60 70 80 90 100
    KTGSFKIRGA LNAIRGLIPD TLEGKPKAVV THSSGNHGQA LTYAAKLEGI
    110 120 130 140 150
    PAYIVVPQTA PNCKKLAIQA YGASIVYSEP SDESRENVAQ RIIQETEGIL
    160 170 180 190 200
    VHPNQEPAVI AGQGTIALEV LNQVPLVDAL VVPVGGGGMV AGIAITIKTL
    210 220 230 240 250
    KPSVKVYAAE PSNADDCYQS KLKGELTPNL HPPETIADGV KSSIGLNTWP
    260 270 280 290 300
    IIRDLVDDVF TVTEDEIKYA TQLVWERMKL LIEPTAGVGL AAVLSQHFQT
    310 320 330
    VSPEVKNICI VLSGGNVDLT SLSWVKQAER PAP
    Length:333
    Mass (Da):35,693
    Last modified:July 5, 2004 - v1
    Checksum:iB0DDD8B7B5A8116C
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB106282 mRNA. Translation: BAC84968.1.
    BC082014 mRNA. Translation: AAH82014.1.
    RefSeqiNP_942052.1. NM_198757.2.
    XP_008766232.1. XM_008768010.1.
    XP_008766233.1. XM_008768011.1.
    XP_008766234.1. XM_008768012.1.
    XP_008766235.1. XM_008768013.1.
    XP_008766236.1. XM_008768014.1.
    XP_008766237.1. XM_008768015.1.
    UniGeneiRn.220332.

    Genome annotation databases

    EnsembliENSRNOT00000046110; ENSRNOP00000050774; ENSRNOG00000002991.
    GeneIDi303306.
    KEGGirno:303306.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB106282 mRNA. Translation: BAC84968.1.
    BC082014 mRNA. Translation: AAH82014.1.
    RefSeqiNP_942052.1. NM_198757.2.
    XP_008766232.1. XM_008768010.1.
    XP_008766233.1. XM_008768011.1.
    XP_008766234.1. XM_008768012.1.
    XP_008766235.1. XM_008768013.1.
    XP_008766236.1. XM_008768014.1.
    XP_008766237.1. XM_008768015.1.
    UniGeneiRn.220332.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3HMKX-ray2.10A/B1-333[»]
    3L6CX-ray2.20A/B1-333[»]
    ProteinModelPortaliQ76EQ0.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi257487. 1 interaction.
    STRINGi10116.ENSRNOP00000050774.

    PTM databases

    PhosphoSiteiQ76EQ0.

    Proteomic databases

    PaxDbiQ76EQ0.
    PRIDEiQ76EQ0.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsembliENSRNOT00000046110; ENSRNOP00000050774; ENSRNOG00000002991.
    GeneIDi303306.
    KEGGirno:303306.

    Organism-specific databases

    CTDi63826.
    RGDi735094. Srr.

    Phylogenomic databases

    eggNOGiCOG1171.
    GeneTreeiENSGT00550000075026.
    HOGENOMiHOG000046974.
    HOVERGENiHBG023167.
    InParanoidiQ76EQ0.
    KOiK12235.
    OMAiWKEEYLT.
    OrthoDBiEOG7HB5B2.
    PhylomeDBiQ76EQ0.
    TreeFamiTF313346.

    Enzyme and pathway databases

    BRENDAi5.1.1.18. 5301.

    Miscellaneous databases

    EvolutionaryTraceiQ76EQ0.
    NextBioi651104.
    PROiQ76EQ0.

    Gene expression databases

    GenevestigatoriQ76EQ0.

    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. "Rat cerebral serine racemase: amino acid deletion and truncation at carboxy terminus."
      Konno R.
      Neurosci. Lett. 349:111-114(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Strain: Sprague-Dawley.
    2. "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: Testis.
    3. "Glia-derived D-serine controls NMDA receptor activity and synaptic memory."
      Panatier A., Theodosis D.T., Mothet J.P., Touquet B., Pollegioni L., Poulain D.A., Oliet S.H.
      Cell 125:775-784(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    4. "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 (2.1 ANGSTROMS) OF 3-333 IN COMPLEX WITH MANGANESE IONS; MALONATE AND PYRIDOXAL PHOSPHATE, COFACTOR, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBUNIT.

    Entry informationi

    Entry nameiSRR_RAT
    AccessioniPrimary (citable) accession number: Q76EQ0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 1, 2007
    Last sequence update: July 5, 2004
    Last modified: March 4, 2015
    This is version 83 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Allosteric enzyme, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. 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.