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Entry version 127 (07 Apr 2021)
Sequence version 1 (01 Jun 2003)
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Protein

Broad specificity amino-acid racemase

Gene

alr

Organism
Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)
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

Amino-acid racemase able to utilize a broad range of substrates. Reversibly racemizes 9 of the 19 natural chiral amino acids known, including both positively charged amino acids (Lys, Arg and His) and non-beta-branched aliphatic amino acids (Ala, Leu, Met, Ser, Gln and Asn). Among these amino acids, activity is the highest with lysine and arginine, and poor or very poor with the others (PubMed:23995642).

Plays a primary role in the catabolism of basic amino acid, that allows P.putida strain KT2440 to grow on L-Lys and L-Arg as the sole source of carbon and nitrogen, through conversion to their respective D-enantiomers (PubMed:30008699).

2 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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'-phosphateUniRule annotation

<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

kcat is 274.5 sec(-1) with D-lysine as substrate. kcat is 1681.7 sec(-1) with L-lysine as substrate. kcat is 8.83 sec(-1) with D-alanine as substrate. kcat is 7.33 sec(-1) with L-alanine as substrate. Thus, the catalytic efficiency with lysine is nearly 3 orders of magnitude greater than that with alanine in both reaction directions.1 Publication
  1. KM=0.36 mM for D-lysine1 Publication
  2. KM=8.96 mM for L-lysine1 Publication
  3. KM=15.71 mM for D-alanine1 Publication
  4. KM=12.62 mM for L-alanine1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 sitei75Proton acceptorUniRule annotation1
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 sitei174SubstrateUniRule annotation1
    Active sitei301Proton acceptorUniRule annotation1
    Binding sitei349Substrate; via amide nitrogenUniRule annotation1

    <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

    <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 functionIsomerase
    LigandPyridoxal phosphate

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    MetaCyc:G1G01-3975-MONOMER
    PPUT160488:G1G01-3975-MONOMER

    <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%5Fand%5Ftaxonomy%5Fsection">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:
    Broad specificity amino-acid racemaseUniRule annotation1 Publication (EC:5.1.1.10UniRule annotation1 Publication)
    Alternative name(s):
    Broad spectrum racemase1 Publication
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:alr1 PublicationImported
    Ordered Locus Names:PP_3722Imported
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiPseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri160488 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
    • UP000000556 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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

    <p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

    Keywords - Cellular componenti

    Periplasm

    <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

    <p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

    Cells lacking this gene exhibit a limited capacity for catabolism of L-Lys and L-Arg as the sole source of carbon and nitrogen. They don't secrete D-Lys in the growth medium. The stationary phase peptidoglycan structure does not differ between wild-type and the deletion mutant strains, indicating that products resulting from this enzyme activity are not incorporated into peptidoglycan under these conditions.1 Publication

    <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 denotes the presence of an N-terminal signal peptide.<p><a href='/help/signal' target='_top'>More...</a></p>Signal peptidei1 – 24UniRule annotationAdd BLAST24
    <p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_500430173025 – 409Broad specificity amino-acid racemaseUniRule annotationAdd BLAST385

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the PTM / Processing":/help/ptm_processing_section section describes the positions of cysteine residues participating in disulfide bonds.<p><a href='/help/disulfid' target='_top'>More...</a></p>Disulfide bondi71 ↔ 97UniRule annotationBy similarity
    <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 residuei75N6-(pyridoxal phosphate)lysineUniRule annotation1

    Keywords - PTMi

    Disulfide bond

    <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

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    160488.PP_3722

    <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
    Q88GJ9

    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

    <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

    Belongs to the alanine racemase family. Bsr subfamily.UniRule annotationCurated

    Keywords - Domaini

    Signal

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    COG0787, Bacteria

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    CLU_028393_1_1_6

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    ETGMGRT

    Family and domain databases

    Conserved Domains Database

    More...
    CDDi
    cd06826, PLPDE_III_AR2, 1 hit

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    2.40.37.10, 1 hit
    3.20.20.10, 1 hit

    HAMAP database of protein families

    More...
    HAMAPi
    MF_02212, Bsr_racemase, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR000821, Ala_racemase
    IPR009006, Ala_racemase/Decarboxylase_C
    IPR011079, Ala_racemase_C
    IPR001608, Ala_racemase_N
    IPR020622, Ala_racemase_pyridoxalP-BS
    IPR029066, PLP-binding_barrel
    IPR043698, Racemase_Bsr/Lyr

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF00842, Ala_racemase_C, 1 hit
    PF01168, Ala_racemase_N, 1 hit

    Protein Motif fingerprint database; a protein domain database

    More...
    PRINTSi
    PR00992, ALARACEMASE

    Simple Modular Architecture Research Tool; a protein domain database

    More...
    SMARTi
    View protein in SMART
    SM01005, Ala_racemase_C, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF50621, SSF50621, 1 hit
    SSF51419, SSF51419, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR00492, alr, 1 hit

    PROSITE; a protein domain and family database

    More...
    PROSITEi
    View protein in PROSITE
    PS00395, ALANINE_RACEMASE, 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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

    Q88GJ9-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MPFRRTLLAA SLALLITGQA PLYAAPPLSM DNGTNTLTVQ NSNAWVEVSA
    60 70 80 90 100
    SALQHNIRTL QAELAGKSKL CAVLKADAYG HGIGLVMPSI IAQGVPCVAV
    110 120 130 140 150
    ASNEEARVVR ASGFTGQLVR VRLASLSELE DGLQYDMEEL VGSAEFARQA
    160 170 180 190 200
    DAIAARHGKT LRIHMALNSS GMSRNGVEMA TWSGRGEALQ ITDQKHLKLV
    210 220 230 240 250
    ALMTHFAVED KDDVRKGLAA FNEQTDWLIK HARLDRSKLT LHAANSFATL
    260 270 280 290 300
    EVPEARLDMV RTGGALFGDT VPARTEYKRA MQFKSHVAAV HSYPAGNTVG
    310 320 330 340 350
    YDRTFTLARD SRLANITVGY SDGYRRVFTN KGHVLINGHR VPVVGKVSMN
    360 370 380 390 400
    TLMVDVTDFP DVKGGNEVVL FGKQAGGEIT QAEMEEINGA LLADLYTVWG

    NSNPKILVD
    Length:409
    Mass (Da):44,224
    Last modified:June 1, 2003 - v1
    <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:i90921393FDBFF5E7
    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
    AE015451 Genomic DNA Translation: AAN69319.1

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_745855.1, NC_002947.4
    WP_010954558.1, NC_002947.4

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    AAN69319; AAN69319; PP_3722

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    ppu:PP_3722

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|160488.4.peg.3967

    <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
    AE015451 Genomic DNA Translation: AAN69319.1
    RefSeqiNP_745855.1, NC_002947.4
    WP_010954558.1, NC_002947.4

    3D structure databases

    SMRiQ88GJ9
    ModBaseiSearch...

    Protein-protein interaction databases

    STRINGi160488.PP_3722

    Genome annotation databases

    EnsemblBacteriaiAAN69319; AAN69319; PP_3722
    KEGGippu:PP_3722
    PATRICifig|160488.4.peg.3967

    Phylogenomic databases

    eggNOGiCOG0787, Bacteria
    HOGENOMiCLU_028393_1_1_6
    OMAiETGMGRT

    Enzyme and pathway databases

    BioCyciMetaCyc:G1G01-3975-MONOMER
    PPUT160488:G1G01-3975-MONOMER

    Family and domain databases

    CDDicd06826, PLPDE_III_AR2, 1 hit
    Gene3Di2.40.37.10, 1 hit
    3.20.20.10, 1 hit
    HAMAPiMF_02212, Bsr_racemase, 1 hit
    InterProiView protein in InterPro
    IPR000821, Ala_racemase
    IPR009006, Ala_racemase/Decarboxylase_C
    IPR011079, Ala_racemase_C
    IPR001608, Ala_racemase_N
    IPR020622, Ala_racemase_pyridoxalP-BS
    IPR029066, PLP-binding_barrel
    IPR043698, Racemase_Bsr/Lyr
    PfamiView protein in Pfam
    PF00842, Ala_racemase_C, 1 hit
    PF01168, Ala_racemase_N, 1 hit
    PRINTSiPR00992, ALARACEMASE
    SMARTiView protein in SMART
    SM01005, Ala_racemase_C, 1 hit
    SUPFAMiSSF50621, SSF50621, 1 hit
    SSF51419, SSF51419, 1 hit
    TIGRFAMsiTIGR00492, alr, 1 hit
    PROSITEiView protein in PROSITE
    PS00395, ALANINE_RACEMASE, 1 hit

    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 nameiBSR_PSEPK
    <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: Q88GJ9
    <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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 8, 2019
    Last sequence update: June 1, 2003
    Last modified: April 7, 2021
    This is version 127 of the entry and version 1 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 programProkaryotic 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
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