Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

P0A6K1

- DAPF_ECOLI

UniProt

P0A6K1 - DAPF_ECOLI

Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 87 (01 Oct 2014)
      Sequence version 1 (29 Mar 2005)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    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

    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

    1. diaminopimelate epimerase activity Source: EcoCyc

    GO - Biological processi

    1. lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP

    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: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10209. dapF.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    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.

    Expressioni

    Gene expression databases

    GenevestigatoriP0A6K1.

    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 – 87
    Beta strandi11 – 177
    Beta strandi19 – 213
    Helixi27 – 348
    Turni36 – 383
    Beta strandi43 – 497
    Beta strandi57 – 648
    Beta strandi69 – 713
    Helixi74 – 8613
    Beta strandi93 – 997
    Beta strandi102 – 1087
    Beta strandi114 – 1174
    Helixi125 – 1273
    Beta strandi137 – 1437
    Beta strandi146 – 16520
    Helixi167 – 1693
    Helixi172 – 1809
    Beta strandi190 – 1989
    Beta strandi201 – 2088
    Turni209 – 2113
    Beta strandi212 – 2154
    Helixi218 – 23013
    Beta strandi236 – 2427
    Beta strandi245 – 2517
    Beta strandi258 – 2625
    Beta strandi265 – 2728

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4IJZX-ray2.00A/B1-274[»]
    4IK0X-ray2.05A/B1-274[»]
    ProteinModelPortaliP0A6K1.
    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.
    KOiK01778.
    OMAiLIVEPPY.
    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

    MQFSKMHGLG NDFMVVDAVT QNVFFSPELI RRLADRHLGV GFDQLLVVEP    50
    PYDPELDFHY RIFNADGSEV AQCGNGARCF ARFVRLKGLT NKRDIRVSTA 100
    NGRMVLTVTD DDLVRVNMGE PNFEPSAVPF RANKAEKTYI MRAAEQTILC 150
    GVVSMGNPHC VIQVDDVDTA AVETLGPVLE SHERFPERAN IGFMQVVKRE 200
    HIRLRVYERG AGETQACGSG ACAAVAVGIQ QGLLAEEVRV ELPGGRLDIA 250
    WKGPGHPLYM TGPAVHVYDG FIHL 274
    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.
    The sequence CAA31413.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

    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:
    EMBL
    GenBank
    DDBJ
    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.
    YP_491632.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76812; AAC76812; b3809.
    BAE77491; BAE77491; BAE77491.
    GeneIDi12934260.
    948364.
    KEGGiecj:Y75_p3368.
    eco:b3809.
    PATRICi32123119. VBIEscCol129921_3925.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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 .
    PIRi B65185. S01913.
    RefSeqi NP_418254.2. NC_000913.3.
    YP_491632.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4IJZ X-ray 2.00 A/B 1-274 [» ]
    4IK0 X-ray 2.05 A/B 1-274 [» ]
    ProteinModelPortali P0A6K1.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-47856N.
    IntActi P0A6K1. 2 interactions.
    STRINGi 511145.b3809.

    Proteomic databases

    PaxDbi P0A6K1.
    PRIDEi P0A6K1.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC76812 ; AAC76812 ; b3809 .
    BAE77491 ; BAE77491 ; BAE77491 .
    GeneIDi 12934260.
    948364.
    KEGGi ecj:Y75_p3368.
    eco:b3809.
    PATRICi 32123119. VBIEscCol129921_3925.

    Organism-specific databases

    EchoBASEi EB0205.
    EcoGenei EG10209. dapF.

    Phylogenomic databases

    eggNOGi COG0253.
    HOGENOMi HOG000220466.
    KOi K01778.
    OMAi LIVEPPY.
    OrthoDBi EOG6ND0M5.
    PhylomeDBi P0A6K1.

    Enzyme and pathway databases

    UniPathwayi UPA00034 ; UER00025 .
    BioCyci EcoCyc:DIAMINOPIMEPIM-MONOMER.
    ECOL316407:JW5592-MONOMER.
    MetaCyc:DIAMINOPIMEPIM-MONOMER.

    Miscellaneous databases

    PROi P0A6K1.

    Gene expression databases

    Genevestigatori P0A6K1.

    Family and domain databases

    HAMAPi MF_00197. DAP_epimerase.
    InterProi IPR018510. DAP_epimerase_AS.
    IPR001653. DAP_epimerase_DapF.
    [Graphical view ]
    PANTHERi PTHR31689. PTHR31689. 1 hit.
    Pfami PF01678. DAP_epimerase. 2 hits.
    [Graphical view ]
    TIGRFAMsi TIGR00652. DapF. 1 hit.
    PROSITEi PS01326. DAP_EPIMERASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 87 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