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Entry version 109 (08 May 2019)
Sequence version 1 (01 Jan 1998)
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Protein

L-Ala-D/L-Glu epimerase

Gene

ykfB

Organism
Bacillus subtilis (strain 168)
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 epimerization of L-Ala-D-Glu to L-Ala-L-Glu and has probably a role in the metabolism of the murein peptide, of which L-Ala-D-Glu is a component. Is also able to catalyze the reverse reaction and the epimerization of the other Ala-X dipeptides L-Ala-L-Asp, L-Ala-L-Leu, L-Ala-L-Met, and L-Ala-L-Ser. Is not able to epimerize other L-Ala-X dipeptides. Is also active with L-Ser-L-Glu and, oddly, L-Pro-L-Glu, but not with L-Glu-L-Glu, L-Lys-L-Glu, L-Lys-L-Ala, or D-Ala-D-Ala.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

Mg2+2 PublicationsNote: Binds 1 Mg2+ ion per subunit.2 Publications

<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

The catalytic efficiency is 25-fold higher with L-Ala-D-Glu than with L-Ala-D-Asp or L-Ala-D-Met as substrate.
  1. KM=320 µM for L-Ala-D-Glu (at pH 8.5)1 Publication
  2. KM=28 µM for L-Ala-D-Asp (at pH 8.5)1 Publication
  3. KM=510 µM for L-Ala-D-Met (at pH 8.5)1 Publication

    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: peptidoglycan degradation

    This protein is involved in the pathway peptidoglycan degradation, which is part of Cell wall degradation.
    View all proteins of this organism that are known to be involved in the pathway peptidoglycan degradation and in Cell wall degradation.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘Function’ 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 sitei24Substrate1 Publication1
    Binding sitei135Substrate1 Publication1
    Binding sitei160Substrate1 Publication1
    <p>This subsection of the ‘Function’ 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 sitei162Proton acceptor; specific for (R)-substrate epimerization1 Publication1
    <p>This subsection of the ‘Function’ 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 bindingi191Magnesium2 Publications1
    Metal bindingi219Magnesium2 Publications1
    Metal bindingi244Magnesium2 Publications1
    Active sitei268Proton acceptor; specific for (S)-substrate epimerization1 Publication1
    Binding sitei296Substrate; via carbonyl oxygen1 Publication1
    Binding sitei298Substrate; via amide nitrogen1 Publication1
    Binding sitei321Substrate1 Publication1
    Binding sitei323Substrate1 Publication1

    <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 functionIsomerase
    Biological processCell wall biogenesis/degradation
    LigandMagnesium, Metal-binding

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    BSUB:BSU12980-MONOMER

    SABIO-RK: Biochemical Reaction Kinetics Database

    More...
    SABIO-RKi
    O34508

    UniPathway: a resource for the exploration and annotation of metabolic pathways

    More...
    UniPathwayi
    UPA00549

    <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:
    L-Ala-D/L-Glu epimerase (EC:5.1.1.201 Publication)
    Short name:
    AE epimerase
    Short name:
    AEE
    <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:ykfB
    Ordered Locus Names:BSU12980
    <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>OrganismiBacillus subtilis (strain 168)
    <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 identifieri224308 [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 lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    <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
    • UP000001570 <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

    <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_00003889701 – 366L-Ala-D/L-Glu epimeraseAdd BLAST366

    Proteomic databases

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

    More...
    PaxDbi
    O34508

    PRoteomics IDEntifications database

    More...
    PRIDEi
    O34508

    <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

    <p>This subsection of the ‘Expression’ section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

    Repressed by AbrB, a transcription factor that negatively controls biofilm formation.1 Publication

    <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

    Homooctamer; tetramer of dimers.2 Publications

    Protein-protein interaction databases

    STRING: functional protein association networks

    More...
    STRINGi
    224308.BSU12980

    <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

    Secondary structure

    1366
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    Select the link destinations:

    Protein Data Bank Europe

    More...
    PDBei

    Protein Data Bank RCSB

    More...
    RCSB PDBi

    Protein Data Bank Japan

    More...
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1JPMX-ray2.25A/B/C/D1-366[»]
    1TKKX-ray2.10A/B/C/D/E/F/G/H1-366[»]

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

    More...
    SMRi
    O34508

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    Miscellaneous databases

    Relative evolutionary importance of amino acids within a protein sequence

    More...
    EvolutionaryTracei
    O34508

    <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

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    ENOG4105DTQ Bacteria
    COG4948 LUCA

    The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

    More...
    HOGENOMi
    HOG000185903

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    O34508

    KEGG Orthology (KO)

    More...
    KOi
    K19802

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    CYSDSSL

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    O34508

    Family and domain databases

    Conserved Domains Database

    More...
    CDDi
    cd03319 L-Ala-DL-Glu_epimerase, 1 hit

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    3.20.20.120, 1 hit
    3.30.390.10, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR034603 Dipeptide_epimerase
    IPR036849 Enolase-like_C_sf
    IPR029017 Enolase-like_N
    IPR029065 Enolase_C-like
    IPR013342 Mandelate_racemase_C
    IPR013341 Mandelate_racemase_N_dom

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF13378 MR_MLE_C, 1 hit
    PF02746 MR_MLE_N, 1 hit

    Structure-Function Linkage Database

    More...
    SFLDi
    SFLDF00010 dipeptide_epimerase, 1 hit

    Simple Modular Architecture Research Tool; a protein domain database

    More...
    SMARTi
    View protein in SMART
    SM00922 MR_MLE, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF51604 SSF51604, 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>.<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.

    O34508-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MKIIRIETSR IAVPLTKPFK TALRTVYTAE SVIVRITYDS GAVGWGEAPP
    60 70 80 90 100
    TLVITGDSMD SIESAIHHVL KPALLGKSLA GYEAILHDIQ HLLTGNMSAK
    110 120 130 140 150
    AAVEMALYDG WAQMCGLPLY QMLGGYRDTL ETDYTVSVNS PEEMAADAEN
    160 170 180 190 200
    YLKQGFQTLK IKVGKDDIAT DIARIQEIRK RVGSAVKLRL DANQGWRPKE
    210 220 230 240 250
    AVTAIRKMED AGLGIELVEQ PVHKDDLAGL KKVTDATDTP IMADESVFTP
    260 270 280 290 300
    RQAFEVLQTR SADLINIKLM KAGGISGAEK INAMAEACGV ECMVGSMIET
    310 320 330 340 350
    KLGITAAAHF AASKRNITRF DFDAPLMLKT DVFNGGITYS GSTISMPGKP
    360
    GLGIIGAALL KGEKEQ
    Length:366
    Mass (Da):39,473
    Last modified:January 1, 1998 - 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:i8E33E7955435CE8B
    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
    AJ002571 Genomic DNA Translation: CAA05578.1
    AL009126 Genomic DNA Translation: CAB13155.1

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    H69855

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_389181.1, NC_000964.3
    WP_003244980.1, NZ_JNCM01000035.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    CAB13155; CAB13155; BSU12980

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    939862

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    bsu:BSU12980

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|224308.179.peg.1410

    <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
    AJ002571 Genomic DNA Translation: CAA05578.1
    AL009126 Genomic DNA Translation: CAB13155.1
    PIRiH69855
    RefSeqiNP_389181.1, NC_000964.3
    WP_003244980.1, NZ_JNCM01000035.1

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1JPMX-ray2.25A/B/C/D1-366[»]
    1TKKX-ray2.10A/B/C/D/E/F/G/H1-366[»]
    SMRiO34508
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi224308.BSU12980

    Proteomic databases

    PaxDbiO34508
    PRIDEiO34508

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAB13155; CAB13155; BSU12980
    GeneIDi939862
    KEGGibsu:BSU12980
    PATRICifig|224308.179.peg.1410

    Phylogenomic databases

    eggNOGiENOG4105DTQ Bacteria
    COG4948 LUCA
    HOGENOMiHOG000185903
    InParanoidiO34508
    KOiK19802
    OMAiCYSDSSL
    PhylomeDBiO34508

    Enzyme and pathway databases

    UniPathwayi
    UPA00549

    BioCyciBSUB:BSU12980-MONOMER
    SABIO-RKiO34508

    Miscellaneous databases

    EvolutionaryTraceiO34508

    Family and domain databases

    CDDicd03319 L-Ala-DL-Glu_epimerase, 1 hit
    Gene3Di3.20.20.120, 1 hit
    3.30.390.10, 1 hit
    InterProiView protein in InterPro
    IPR034603 Dipeptide_epimerase
    IPR036849 Enolase-like_C_sf
    IPR029017 Enolase-like_N
    IPR029065 Enolase_C-like
    IPR013342 Mandelate_racemase_C
    IPR013341 Mandelate_racemase_N_dom
    PfamiView protein in Pfam
    PF13378 MR_MLE_C, 1 hit
    PF02746 MR_MLE_N, 1 hit
    SFLDiSFLDF00010 dipeptide_epimerase, 1 hit
    SMARTiView protein in SMART
    SM00922 MR_MLE, 1 hit
    SUPFAMiSSF51604 SSF51604, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    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 nameiAEEP_BACSU
    <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: O34508
    Secondary accession number(s): Q796M5
    <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 24, 2009
    Last sequence update: January 1, 1998
    Last modified: May 8, 2019
    This is version 109 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

    3D-structure, 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
    3. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    4. PATHWAY comments
      Index of metabolic and biosynthesis pathways
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