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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. Only accepts DAP isomers with the L configuration.3 Publications

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.2 Publications

Enzyme regulationi

Inhibited by 2-(4-amino-4-carboxybutyl)aziri-dine-2-carboxylate (aziDAP) and iodoacetamide.3 Publications

Kineticsi

  1. KM=0.16 mM for D,L-DAP (at pH 7.8 and at 25 degrees Celsius)2 Publications
  2. KM=0.26 mM for L,L-DAP (at pH 7.8 and at 25 degrees Celsius)2 Publications
  3. KM=0.36 mM for L,L-DAP (at pH 7.8 and at 25 degrees Celsius)2 Publications

    Pathwayi: L-lysine biosynthesis via DAP pathway

    This protein is involved in step 1 of the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate.
    Proteins known to be involved in this subpathway in this organism are:
    1. Diaminopimelate epimerase (dapF)
    This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes DL-2,6-diaminopimelate from LL-2,6-diaminopimelate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei11SubstrateBy similarity1
    Binding sitei44SubstrateBy similarity1
    Binding sitei64SubstrateBy similarity1
    Active sitei73Proton donor/acceptorBy similarity1
    Binding sitei157SubstrateBy similarity1
    Sitei159Important for catalytic activitySequence analysis1
    Binding sitei190SubstrateBy similarity1
    Sitei208Important for catalytic activitySequence analysis1
    Active sitei217Proton donor/acceptorBy similarity1

    GO - Molecular functioni

    • diaminopimelate epimerase activity Source: EcoCyc

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Amino-acid biosynthesis, Lysine biosynthesis

    Enzyme and pathway databases

    BioCyciEcoCyc:DIAMINOPIMEPIM-MONOMER.
    ECOL316407:JW5592-MONOMER.
    MetaCyc:DIAMINOPIMEPIM-MONOMER.
    UniPathwayiUPA00034; UER00025.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Diaminopimelate epimerase (EC:5.1.1.7)
    Short name:
    DAP epimerase
    Gene namesi
    Name:dapF
    Ordered Locus Names:b3809, JW5592
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10209. dapF.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001498381 – 274Diaminopimelate epimeraseAdd BLAST274

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Disulfide bondi73 ↔ 217By similarity

    Keywords - PTMi

    Disulfide bond

    Proteomic databases

    PaxDbiP0A6K1.
    PRIDEiP0A6K1.

    Interactioni

    Subunit structurei

    Monomer.1 Publication

    Protein-protein interaction databases

    DIPiDIP-47856N.
    IntActiP0A6K1. 2 interactors.
    STRINGi511145.b3809.

    Structurei

    Secondary structure

    1274
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi2 – 8Combined sources7
    Beta strandi11 – 17Combined sources7
    Beta strandi19 – 21Combined sources3
    Helixi27 – 34Combined sources8
    Turni36 – 38Combined sources3
    Beta strandi43 – 49Combined sources7
    Beta strandi57 – 64Combined sources8
    Beta strandi69 – 71Combined sources3
    Helixi74 – 86Combined sources13
    Beta strandi93 – 99Combined sources7
    Beta strandi102 – 108Combined sources7
    Beta strandi114 – 117Combined sources4
    Helixi125 – 127Combined sources3
    Beta strandi137 – 143Combined sources7
    Beta strandi146 – 165Combined sources20
    Helixi167 – 169Combined sources3
    Helixi172 – 180Combined sources9
    Beta strandi190 – 198Combined sources9
    Beta strandi201 – 208Combined sources8
    Turni209 – 211Combined sources3
    Beta strandi212 – 215Combined sources4
    Helixi218 – 230Combined sources13
    Beta strandi236 – 242Combined sources7
    Beta strandi245 – 251Combined sources7
    Beta strandi258 – 262Combined sources5
    Beta strandi265 – 272Combined sources8

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4IJZX-ray2.00A/B1-274[»]
    4IK0X-ray2.05A/B1-274[»]
    ProteinModelPortaliP0A6K1.
    SMRiP0A6K1.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni8 – 9SubstrateBy similarity2
    Regioni73 – 75Substrate bindingBy similarity3
    Regioni208 – 209Substrate bindingBy similarity2
    Regioni218 – 219Substrate bindingBy similarity2

    Sequence similaritiesi

    Belongs to the diaminopimelate epimerase family.Curated

    Phylogenomic databases

    eggNOGiENOG4105E4Z. Bacteria.
    COG0253. LUCA.
    HOGENOMiHOG000220466.
    InParanoidiP0A6K1.
    KOiK01778.
    OMAiRFTKMQG.
    PhylomeDBiP0A6K1.

    Family and domain databases

    HAMAPiMF_00197. DAP_epimerase. 1 hit.
    InterProiIPR018510. DAP_epimerase_AS.
    IPR001653. DAP_epimerase_DapF.
    [Graphical view]
    PANTHERiPTHR31689. PTHR31689. 1 hit.
    PfamiPF01678. DAP_epimerase. 2 hits.
    [Graphical view]
    TIGRFAMsiTIGR00652. DapF. 1 hit.
    PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P0A6K1-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MQFSKMHGLG NDFMVVDAVT QNVFFSPELI RRLADRHLGV GFDQLLVVEP
    60 70 80 90 100
    PYDPELDFHY RIFNADGSEV AQCGNGARCF ARFVRLKGLT NKRDIRVSTA
    110 120 130 140 150
    NGRMVLTVTD DDLVRVNMGE PNFEPSAVPF RANKAEKTYI MRAAEQTILC
    160 170 180 190 200
    GVVSMGNPHC VIQVDDVDTA AVETLGPVLE SHERFPERAN IGFMQVVKRE
    210 220 230 240 250
    HIRLRVYERG AGETQACGSG ACAAVAVGIQ QGLLAEEVRV ELPGGRLDIA
    260 270
    WKGPGHPLYM TGPAVHVYDG FIHL
    Length:274
    Mass (Da):30,209
    Last modified:March 29, 2005 - v1
    Checksum:i4ACC137D2F5BD240
    GO

    Sequence cautioni

    The sequence AAA67605 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
    The sequence CAA31413 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti98S → T in CAA31413 (PubMed:3057443).Curated1
    Sequence conflicti160 – 161CV → WL in CAA31413 (PubMed:3057443).Curated2
    Sequence conflicti200 – 201EH → DD in CAA31413 (PubMed:3057443).Curated2

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X12968 Genomic DNA. Translation: CAA31413.1. Different initiation.
    M87049 Genomic DNA. Translation: AAA67605.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC76812.2.
    AP009048 Genomic DNA. Translation: BAE77491.1.
    M38257 Genomic DNA. Translation: AAA24761.1.
    X66782 Genomic DNA. Translation: CAA47282.1.
    PIRiB65185. S01913.
    RefSeqiNP_418254.2. NC_000913.3.
    WP_001160654.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76812; AAC76812; b3809.
    BAE77491; BAE77491; BAE77491.
    GeneIDi948364.
    KEGGiecj:JW5592.
    eco:b3809.
    PATRICi32123119. VBIEscCol129921_3925.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X12968 Genomic DNA. Translation: CAA31413.1. Different initiation.
    M87049 Genomic DNA. Translation: AAA67605.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC76812.2.
    AP009048 Genomic DNA. Translation: BAE77491.1.
    M38257 Genomic DNA. Translation: AAA24761.1.
    X66782 Genomic DNA. Translation: CAA47282.1.
    PIRiB65185. S01913.
    RefSeqiNP_418254.2. NC_000913.3.
    WP_001160654.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4IJZX-ray2.00A/B1-274[»]
    4IK0X-ray2.05A/B1-274[»]
    ProteinModelPortaliP0A6K1.
    SMRiP0A6K1.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-47856N.
    IntActiP0A6K1. 2 interactors.
    STRINGi511145.b3809.

    Proteomic databases

    PaxDbiP0A6K1.
    PRIDEiP0A6K1.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76812; AAC76812; b3809.
    BAE77491; BAE77491; BAE77491.
    GeneIDi948364.
    KEGGiecj:JW5592.
    eco:b3809.
    PATRICi32123119. VBIEscCol129921_3925.

    Organism-specific databases

    EchoBASEiEB0205.
    EcoGeneiEG10209. dapF.

    Phylogenomic databases

    eggNOGiENOG4105E4Z. Bacteria.
    COG0253. LUCA.
    HOGENOMiHOG000220466.
    InParanoidiP0A6K1.
    KOiK01778.
    OMAiRFTKMQG.
    PhylomeDBiP0A6K1.

    Enzyme and pathway databases

    UniPathwayiUPA00034; UER00025.
    BioCyciEcoCyc:DIAMINOPIMEPIM-MONOMER.
    ECOL316407:JW5592-MONOMER.
    MetaCyc:DIAMINOPIMEPIM-MONOMER.

    Miscellaneous databases

    PROiP0A6K1.

    Family and domain databases

    HAMAPiMF_00197. DAP_epimerase. 1 hit.
    InterProiIPR018510. DAP_epimerase_AS.
    IPR001653. DAP_epimerase_DapF.
    [Graphical view]
    PANTHERiPTHR31689. PTHR31689. 1 hit.
    PfamiPF01678. DAP_epimerase. 2 hits.
    [Graphical view]
    TIGRFAMsiTIGR00652. DapF. 1 hit.
    PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDAPF_ECOLI
    AccessioniPrimary (citable) accession number: P0A6K1
    Secondary accession number(s): P08885
    , P78126, Q2M8B5, Q8X8P8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 29, 2005
    Last sequence update: March 29, 2005
    Last modified: November 2, 2016
    This is version 100 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    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 one 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.