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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

    Pathway: 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), 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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei11 – 111SubstrateBy similarity
    Binding sitei44 – 441SubstrateBy similarity
    Binding sitei64 – 641SubstrateBy similarity
    Active sitei73 – 731Proton donor/acceptorBy similarity
    Binding sitei157 – 1571SubstrateBy similarity
    Sitei159 – 1591Important for catalytic activitySequence Analysis
    Binding sitei190 – 1901SubstrateBy similarity
    Sitei208 – 2081Important for catalytic activitySequence Analysis
    Active sitei217 – 2171Proton donor/acceptorBy similarity

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10209. dapF.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 274274Diaminopimelate epimerasePRO_0000149838Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    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 interactions.
    STRINGi511145.b3809.

    Structurei

    Secondary structure

    1
    274
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 87Combined sources
    Beta strandi11 – 177Combined sources
    Beta strandi19 – 213Combined sources
    Helixi27 – 348Combined sources
    Turni36 – 383Combined sources
    Beta strandi43 – 497Combined sources
    Beta strandi57 – 648Combined sources
    Beta strandi69 – 713Combined sources
    Helixi74 – 8613Combined sources
    Beta strandi93 – 997Combined sources
    Beta strandi102 – 1087Combined sources
    Beta strandi114 – 1174Combined sources
    Helixi125 – 1273Combined sources
    Beta strandi137 – 1437Combined sources
    Beta strandi146 – 16520Combined sources
    Helixi167 – 1693Combined sources
    Helixi172 – 1809Combined sources
    Beta strandi190 – 1989Combined sources
    Beta strandi201 – 2088Combined sources
    Turni209 – 2113Combined sources
    Beta strandi212 – 2154Combined sources
    Helixi218 – 23013Combined sources
    Beta strandi236 – 2427Combined sources
    Beta strandi245 – 2517Combined sources
    Beta strandi258 – 2625Combined sources
    Beta strandi265 – 2728Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4IJZX-ray2.00A/B1-274[»]
    4IK0X-ray2.05A/B1-274[»]
    ProteinModelPortaliP0A6K1.
    SMRiP0A6K1. Positions 1-274.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni8 – 92SubstrateBy similarity
    Regioni73 – 753Substrate bindingBy similarity
    Regioni208 – 2092Substrate bindingBy similarity
    Regioni218 – 2192Substrate bindingBy similarity

    Sequence similaritiesi

    Belongs to the diaminopimelate epimerase family.Curated

    Phylogenomic databases

    eggNOGiCOG0253.
    HOGENOMiHOG000220466.
    InParanoidiP0A6K1.
    KOiK01778.
    OMAiMKFTKMH.
    OrthoDBiEOG6ND0M5.
    PhylomeDBiP0A6K1.

    Family and domain databases

    HAMAPiMF_00197. DAP_epimerase.
    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 AAA67605.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
    The sequence CAA31413.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti98 – 981S → T in CAA31413 (PubMed:3057443).Curated
    Sequence conflicti160 – 1612CV → WL in CAA31413 (PubMed:3057443).Curated
    Sequence conflicti200 – 2012EH → DD in CAA31413 (PubMed:3057443).Curated

    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.

    Genome annotation databases

    EnsemblBacteriaiAAC76812; AAC76812; b3809.
    BAE77491; BAE77491; BAE77491.
    GeneIDi948364.
    KEGGiecj:Y75_p3368.
    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.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4IJZX-ray2.00A/B1-274[»]
    4IK0X-ray2.05A/B1-274[»]
    ProteinModelPortaliP0A6K1.
    SMRiP0A6K1. Positions 1-274.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

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

    Proteomic databases

    PaxDbiP0A6K1.
    PRIDEiP0A6K1.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC76812; AAC76812; b3809.
    BAE77491; BAE77491; BAE77491.
    GeneIDi948364.
    KEGGiecj:Y75_p3368.
    eco:b3809.
    PATRICi32123119. VBIEscCol129921_3925.

    Organism-specific databases

    EchoBASEiEB0205.
    EcoGeneiEG10209. dapF.

    Phylogenomic databases

    eggNOGiCOG0253.
    HOGENOMiHOG000220466.
    InParanoidiP0A6K1.
    KOiK01778.
    OMAiMKFTKMH.
    OrthoDBiEOG6ND0M5.
    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.
    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...

    Publicationsi

    « Hide 'large scale' publications
    1. "Nucleotide sequence of the dapF gene and flanking regions from Escherichia coli K12."
      Richaud C., Printz C.
      Nucleic Acids Res. 16:10367-10367(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. "Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes."
      Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.
      Science 257:771-778(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "Recombination at ColE1 cer requires the Escherichia coli xerC gene product, a member of the lambda integrase family of site-specific recombinases."
      Colloms S.D., Sykora P., Szatmari G., Sherratt D.J.
      J. Bacteriol. 172:6973-6980(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 259-274.
      Strain: K12.
    6. "Comparative analysis of the cya locus in enterobacteria and related Gram-negative facultative anaerobes."
      Trotot P., Sismeiro O., Vivares C., Glaser P., Bresson-Roy A., Danchin A.
      Biochimie 78:277-287(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-8.
      Strain: K12.
    7. "Purification and properties of diaminopimelic acid epimerase from Escherichia coli."
      Wiseman J.S., Nichols J.S.
      J. Biol. Chem. 259:8907-8914(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
    8. "Molecular cloning, characterization, and chromosomal localization of dapF, the Escherichia coli gene for diaminopimelate epimerase."
      Richaud C., Higgins W., Mengin-Lecreulx D., Stragier P.
      J. Bacteriol. 169:1454-1459(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    9. "Analogs of diaminopimelic acid as inhibitors of meso-diaminopimelate dehydrogenase and LL-diaminopimelate epimerase."
      Lam L.K., Arnold L.D., Kalantar T.H., Kelland J.G., Lane-Bell P.M., Palcic M.M., Pickard M.A., Vederas J.C.
      J. Biol. Chem. 263:11814-11819(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
    10. "2-(4-Amino-4-carboxybutyl)aziridine-2-carboxylic acid. A potent irreversible inhibitor of diaminopimelic acid epimerase. Spontaneous formation from alpha-(halomethyl)diaminopimelic acids."
      Gerhart F., Higgins W., Tardif C., Ducep J.B.
      J. Med. Chem. 33:2157-2162(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: ENZYME REGULATION.

    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: June 24, 2015
    This is version 94 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

    External Data

    Dasty 3

    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 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.