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Entry version 91 (11 Dec 2019)
Sequence version 1 (22 Aug 2006)
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Protein

D-Ala-D/L-Ala epimerase

Gene

tfdD

Organism
Cytophaga hutchinsonii (strain ATCC 33406 / NCIMB 9469)
Status
Reviewed-Annotation score:

Annotation score:4 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 D-Ala-D-Ala to D-Ala-L-Ala. Has broad substrate specificity and catalyzes the epimerization of a variety of dipeptides containing an N-terminal Ala followed by a hydrophobic or polar residue, such as Val, Ser and Met (in vitro).1 Publication

Miscellaneous

Part of a large, functionally divergent protein family. Protein modeling and substrate docking were used to predict the substrate specificity, prior to biochemical analysis.

<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+1 PublicationNote: Binds 1 Mg2+ ion per subunit.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

kcat is 43 sec(-1) for epimerization of D-Ala-D-Ala. kcat is 58 sec(-1) for epimerization of D-Ala-L-Ala. kcat is 19 sec(-1) for epimerization of D-Ala-L-Val. kcat is 37 sec(-1) for epimerization of L-Ala-L-Ala.
  1. KM=1.1 mM for D-Ala-L-Ala1 Publication
  2. KM=1.9 mM for D-Ala-D-Ala1 Publication
  3. KM=0.5 mM for D-Ala-L-Val1 Publication
  4. KM=5.0 mM for L-Ala-L-Ala1 Publication

    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 sitei135Substrate1
    <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 bindingi190Magnesium1
    Metal bindingi216Magnesium1
    Metal bindingi241Magnesium1
    Binding sitei265Substrate1

    <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
    LigandMagnesium, Metal-binding

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    CHUT269798:G1G6N-2103-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_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:
    D-Ala-D/L-Ala epimerase (EC:5.1.1.-)
    <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:tfdD
    Ordered Locus Names:CHU_2140
    <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>OrganismiCytophaga hutchinsonii (strain ATCC 33406 / NCIMB 9469)
    <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 identifieri269798 [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 lineageiBacteriaBacteroidetesCytophagiaCytophagalesCytophagaceaeCytophaga
    <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
    • UP000001822 <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_00004296441 – 368D-Ala-D/L-Ala epimeraseAdd BLAST368

    <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
    269798.CHU_2140

    <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

    1368
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

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

    More...
    SMRi
    Q11T61

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    Protein Data Bank in Europe - Knowledge Base

    More...
    PDBe-KBi
    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>Regioni160 – 162Substrate binding3
    Regioni318 – 320Substrate binding3

    <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

    KEGG Orthology (KO)

    More...
    KOi
    K19802

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    FGCYSDS

    Database of Orthologous Groups

    More...
    OrthoDBi
    951991at2

    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

    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
    SSF54826 SSF54826, 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.

    Q11T61-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MIITQVELYK SPVKLKEPFK ISLGILTHAN NVIVRIHTAS GHIGYGECSP
    60 70 80 90 100
    FMTIHGESMD TAFIVGQYLA KGLIGTSCLD IVSNSLLMDA IIYGNSCIKS
    110 120 130 140 150
    AFNIALYDLA AQHAGLPLYA FLGGKKDKII QTDYTVSIDE PHKMAADAVQ
    160 170 180 190 200
    IKKNGFEIIK VKVGGSKELD VERIRMIREA AGDSITLRID ANQGWSVETA
    210 220 230 240 250
    IETLTLLEPY NIQHCEEPVS RNLYTALPKI RQACRIPIMA DESCCNSFDA
    260 270 280 290 300
    ERLIQIQACD SFNLKLSKSA GITNALNIIR LAEQAHMPVQ VGGFLESRLG
    310 320 330 340 350
    FTAAAHVALV SKTICYYDFD TPLMFEADPV RGGIVYQQRG IIEVPETAGL
    360
    GAGYQKDYLS GLEKICIN
    Length:368
    Mass (Da):40,311
    Last modified:August 22, 2006 - 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:i1884D7929CF22AB8
    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
    CP000383 Genomic DNA Translation: ABG59403.1

    NCBI Reference Sequences

    More...
    RefSeqi
    WP_011585520.1, NZ_FPJX01000013.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    ABG59403; ABG59403; CHU_2140

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    chu:CHU_2140

    <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
    CP000383 Genomic DNA Translation: ABG59403.1
    RefSeqiWP_011585520.1, NZ_FPJX01000013.1

    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
    3Q45X-ray3.00A/B/C/D/E/F/G/H/I1-368[»]
    3Q4DX-ray3.00A/B/C/D/E/F/G/H/I1-368[»]
    SMRiQ11T61
    ModBaseiSearch...
    PDBe-KBiSearch...

    Protein-protein interaction databases

    STRINGi269798.CHU_2140

    Genome annotation databases

    EnsemblBacteriaiABG59403; ABG59403; CHU_2140
    KEGGichu:CHU_2140

    Phylogenomic databases

    eggNOGiENOG4105DTQ Bacteria
    COG4948 LUCA
    HOGENOMiHOG000185903
    KOiK19802
    OMAiFGCYSDS
    OrthoDBi951991at2

    Enzyme and pathway databases

    BioCyciCHUT269798:G1G6N-2103-MONOMER

    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
    SMARTiView protein in SMART
    SM00922 MR_MLE, 1 hit
    SUPFAMiSSF51604 SSF51604, 1 hit
    SSF54826 SSF54826, 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 nameiAAEP_CYTH3
    <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: Q11T61
    <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: July 9, 2014
    Last sequence update: August 22, 2006
    Last modified: December 11, 2019
    This is version 91 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, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
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