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Entry version 109 (11 Dec 2019)
Sequence version 2 (01 Mar 2004)
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Protein

Serine racemase

Gene

SERR

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Catalyzes the synthesis of D-serine from L-serine. Has dehydratase activity towards both L-serine and D-serine.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

pyridoxal 5'-phosphate

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes regulatory mechanisms for enzymes, transporters or microbial transcription factors, and reports the components which regulate (by activation or inhibition) the reaction.<p><a href='/help/activity_regulation' target='_top'>More...</a></p>Activity regulationi

Inhibited by semicarbazide, hydroxylamine, aminooxyacetate, sodium borate or phenylhydrazine. Racemase activity is enhanced by Ca2+, Mg2+ and is decreased by ATP, Cu2+, Zn2+. Hydratase activity is enhanced by ATP and is decreased by Ca2+, Mg2+, Co2+, Cu2+, Ni2+, Zn2+.1 Publication

<p>This subsection of the ‘Function’ section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

  1. KM=18 mM for L-serine (racemase activity)2 Publications
  2. KM=20 mM for D-serine (racemase activity)2 Publications
  3. KM=28 mM for L-serine (dehydratase activity)2 Publications
  4. KM=19 mM for L-serine (dehydratase activity)2 Publications

    pH dependencei

    Optimum pH is 9.5 for racemization and 9.0 for hydration.2 Publications

    Temperature dependencei

    Optimum temperature is 35 degrees Celsius (racemase or dehydratase activity).2 Publications

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei63ATPBy similarity1
    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei68Proton acceptorBy similarity1
    Active sitei93Proton acceptorBy similarity1
    Binding sitei130ATPBy similarity1
    Binding sitei144SubstrateBy similarity1
    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi219Magnesium1
    Metal bindingi223Magnesium; via carbonyl oxygenBy similarity1
    Metal bindingi225Magnesium1

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    GO - Biological processi

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

    Molecular functionAllosteric enzyme, Isomerase, Lyase
    LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding, Pyridoxal phosphate

    Enzyme and pathway databases

    BRENDA Comprehensive Enzyme Information System

    More...
    BRENDAi
    5.1.1.18 4460

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:SERR
    Ordered Locus Names:Os04g0555900, LOC_Os04g46930
    ORF Names:OsJ_15733, OSJNBb0012E24.7
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiOryza sativa subsp. japonica (Rice)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri39947 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliopsidaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryzaOryza sativa
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
    • UP000059680 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 4

    <p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi219E → A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-225. 1 Publication1
    Mutagenesisi225D → A: Reduces catalytic activity and abolishes the regulatory effect of Mg(2+) addition; when associated with A-219. 1 Publication1

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00004203481 – 339Serine racemaseAdd BLAST339

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei68N6-(pyridoxal phosphate)lysineBy similarity1
    Modified residuei122S-nitrosocysteineBy similarity1

    Keywords - PTMi

    S-nitrosylation

    Proteomic databases

    PaxDb, a database of protein abundance averages across all three domains of life

    More...
    PaxDbi
    Q7XSN8

    <p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

    Gene expression databases

    Genevisible search portal to normalized and curated expression data from Genevestigator

    More...
    Genevisiblei
    Q7XSN8 OS

    <p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

    <p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

    Homodimer.

    1 Publication

    GO - Molecular functioni

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    4530.OS04T0555900-01

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    3D structure databases

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...
    SMRi
    Q7XSN8

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni246 – 247Substrate bindingBy similarity2

    <p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    KOG1251 Eukaryota
    COG1171 LUCA

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    Q7XSN8

    KEGG Orthology (KO)

    More...
    KOi
    K12235

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    LIHPFDH

    Database of Orthologous Groups

    More...
    OrthoDBi
    943371at2759

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    3.40.50.1100, 2 hits

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR001926 PLP-dep
    IPR036052 Trypto_synt_PLP_dependent

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF00291 PALP, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF53686 SSF53686, 1 hit

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

    Q7XSN8-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MGSRGGSGGD GAESHGYAAD IHSIREAQAR IAPYVHKTPV LSSTSIDAIV
    60 70 80 90 100
    GKQLFFKCEC FQKAGAFKIR GASNSIFALD DDEASKGVVT HSSGNHAAAV
    110 120 130 140 150
    ALAAKLRGIP AYIVIPRNAP ACKVDNVKRY GGHIIWSDVS IESRESVAKR
    160 170 180 190 200
    VQEETGAILV HPFNNKNTIS GQGTVSLELL EEVPEIDTII VPISGGGLIS
    210 220 230 240 250
    GVALAAKAIN PSIRILAAEP KGADDSAQSK AAGKIITLPS TNTIADGLRA
    260 270 280 290 300
    FLGDLTWPVV RDLVDDIIVV DDNAIVDAMK MCYEMLKVAV EPSGAIGLAA
    310 320 330
    ALSDEFKQSS AWHESSKIGI IVSGGNVDLG VLWESLYKR
    Length:339
    Mass (Da):35,597
    Last modified:March 1, 2004 - v2
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i71C28D4F16C23875
    GO

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...
    EMBLi

    GenBank nucleotide sequence database

    More...
    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...
    DDBJi
    Links Updated
    AB425957 mRNA Translation: BAH59439.1
    AL606647 Genomic DNA Translation: CAE01865.2
    AP008210 Genomic DNA Translation: BAF15435.1
    AP014960 Genomic DNA Translation: BAS90428.1
    CM000141 Genomic DNA Translation: EAZ31592.1
    AK063168 mRNA Translation: BAG88574.1

    NCBI Reference Sequences

    More...
    RefSeqi
    XP_015637224.1, XM_015781738.1
    XP_015637225.1, XM_015781739.1
    XP_015637226.1, XM_015781740.1
    XP_015637227.1, XM_015781741.1
    XP_015637228.1, XM_015781742.1

    Genome annotation databases

    Ensembl plant genome annotation project

    More...
    EnsemblPlantsi
    Os04t0555900-01; Os04t0555900-01; Os04g0555900

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    4336624

    Gramene; a comparative resource for plants

    More...
    Gramenei
    Os04t0555900-01; Os04t0555900-01; Os04g0555900

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    osa:4336624

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB425957 mRNA Translation: BAH59439.1
    AL606647 Genomic DNA Translation: CAE01865.2
    AP008210 Genomic DNA Translation: BAF15435.1
    AP014960 Genomic DNA Translation: BAS90428.1
    CM000141 Genomic DNA Translation: EAZ31592.1
    AK063168 mRNA Translation: BAG88574.1
    RefSeqiXP_015637224.1, XM_015781738.1
    XP_015637225.1, XM_015781739.1
    XP_015637226.1, XM_015781740.1
    XP_015637227.1, XM_015781741.1
    XP_015637228.1, XM_015781742.1

    3D structure databases

    SMRiQ7XSN8
    ModBaseiSearch...

    Protein-protein interaction databases

    STRINGi4530.OS04T0555900-01

    Proteomic databases

    PaxDbiQ7XSN8

    Genome annotation databases

    EnsemblPlantsiOs04t0555900-01; Os04t0555900-01; Os04g0555900
    GeneIDi4336624
    GrameneiOs04t0555900-01; Os04t0555900-01; Os04g0555900
    KEGGiosa:4336624

    Phylogenomic databases

    eggNOGiKOG1251 Eukaryota
    COG1171 LUCA
    InParanoidiQ7XSN8
    KOiK12235
    OMAiLIHPFDH
    OrthoDBi943371at2759

    Enzyme and pathway databases

    BRENDAi5.1.1.18 4460

    Gene expression databases

    GenevisibleiQ7XSN8 OS

    Family and domain databases

    Gene3Di3.40.50.1100, 2 hits
    InterProiView protein in InterPro
    IPR001926 PLP-dep
    IPR036052 Trypto_synt_PLP_dependent
    PfamiView protein in Pfam
    PF00291 PALP, 1 hit
    SUPFAMiSSF53686 SSF53686, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiSRR_ORYSJ
    <p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q7XSN8
    Secondary accession number(s): A0A0P0WDF8
    <p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 28, 2012
    Last sequence update: March 1, 2004
    Last modified: December 11, 2019
    This is version 109 of the entry and version 2 of the sequence. See complete history.
    <p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    <p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. Oryza sativa (rice)
      Index of Oryza sativa entries and their corresponding gene designations
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