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Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
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 (PubMed:10194362, PubMed:16723397). Only accepts DAP isomers with the L configuration (PubMed:16723397).2 Publications

Miscellaneous

DapF utilizes a two-base mechanism involving a pair of cysteine residues (Cys-73 and Cys-217).1 Publication

Catalytic activityi

LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.1 Publication

Enzyme regulationi

Inhibited by LL-aziridino (LL-AziDAP), DL-aziridino (DL-AziDAP) (PubMed:16723397). Also inhibited by (2S,3R,6S)-2,6-diamino-3-fluoropimelate (L,L-3-fluoro-DAP) and (2R,3S,6S)-2,6-diamino-3-fluoropimelate (D,L-3-fluoro-DAP) (Ref. 3).2 Publications

Kineticsi

Kcat is 128 and 82 sec(-1) for L,L-DAP and D,L-DAP, respectively.1 Publication
  1. KM=0.7 mM for L,L-DAP (at pH 7.8)1 Publication
  2. KM=1.1 mM for D,L-DAP (at pH 7.8)1 Publication

    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.Curated
    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 sitei11SubstrateCombined sources1 Publication1
    Binding sitei44SubstrateCombined sources1 Publication1
    Binding sitei64SubstrateCombined sources1 Publication1
    Active sitei73Proton donorCombined sources3 Publications1
    Binding sitei157SubstrateCombined sources1 Publication1
    Sitei159Could be important to modulate the pK values of the two catalytic cysteine residuesCombined sources1 Publication1
    Binding sitei190SubstrateCombined sources1 Publication1
    Sitei208Could be important to modulate the pK values of the two catalytic cysteine residuesCombined sources1 Publication1
    Active sitei217Proton acceptorCombined sources3 Publications1
    Sitei268Important for dimerizationBy similarity1

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

    Molecular functionIsomerase
    Biological processAmino-acid biosynthesis, Lysine biosynthesis

    Enzyme and pathway databases

    BRENDAi5.1.1.7. 2529.
    UniPathwayiUPA00034; UER00025.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Diaminopimelate epimerase1 Publication (EC:5.1.1.71 Publication)
    Short name:
    DAP epimerase1 Publication
    Alternative name(s):
    PLP-independent amino acid racemase1 Publication
    Gene namesi
    Name:dapF1 Publication
    Ordered Locus Names:HI_0750
    OrganismiHaemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
    Taxonomic identifieri71421 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPasteurellalesPasteurellaceaeHaemophilus
    Proteomesi
    • UP000000579 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi73C → A: Inactive as epimerase, but it is able to rapidly catalyze the HF elimination via abstraction of the C-2 hydrogen of the D,L-3-fluoro-DAP analog and is essentially unable to catalyze the same elimination with the L,L-3-fluoro-DAP analog. 1 Publication1
    Mutagenesisi73C → S: Enzymatically active, but it adopts a more open conformation. It is able to catalyze both epimerization of DAP and HF elimination of L,L-3-fluoro-DAP and D,L-3-fluoro-DAP. Able to slowly eliminate HF but does not catalyze epimerization; when associated with S-217. 2 Publications1
    Mutagenesisi217C → A: Inactive as epimerase. It is able to rapidly catalyze the HF elimination via abstraction of the C-2 hydrogen of the L,L-3-fluoro-DAP analog and is essentially unable to catalyze the same elimination with the D,L-3-fluoro-DAP analog. 1 Publication1
    Mutagenesisi217C → S: Enzymatically active, but it adopts a more open conformation. It is able to catalyze both epimerization of DAP and HF elimination of L,L-3-fluoro-DAP and D,L-3-fluoro-DAP. Able to slowly eliminate HF but does not catalyze epimerization; when associated with S-73. 2 Publications1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001498421 – 274Diaminopimelate epimeraseAdd BLAST274

    Interactioni

    Subunit structurei

    Homodimer (Potential). Previously DapF has been proposed to be a monomer, however it seems that it adopts a dimeric structure (PubMed:9843410, PubMed:17889830).UniRule annotation2 Publications

    Protein-protein interaction databases

    STRINGi71421.HI0750.

    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 strandi56 – 64Combined sources9
    Beta strandi69 – 71Combined sources3
    Helixi74 – 86Combined sources13
    Beta strandi93 – 98Combined sources6
    Beta strandi103 – 108Combined sources6
    Beta strandi114 – 117Combined sources4
    Helixi125 – 127Combined sources3
    Beta strandi137 – 142Combined sources6
    Beta strandi147 – 163Combined sources17
    Turni167 – 169Combined sources3
    Helixi172 – 180Combined sources9
    Beta strandi190 – 198Combined sources9
    Beta strandi201 – 208Combined sources8
    Turni209 – 211Combined sources3
    Helixi218 – 230Combined sources13
    Beta strandi236 – 242Combined sources7
    Beta strandi245 – 251Combined sources7
    Beta strandi258 – 262Combined sources5
    Beta strandi265 – 271Combined sources7

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1BWZX-ray2.72A1-274[»]
    1GQZX-ray1.75A1-274[»]
    2GKEX-ray1.35A1-274[»]
    2GKJX-ray1.70A1-274[»]
    2Q9HX-ray2.30A1-274[»]
    2Q9JX-ray2.20A1-274[»]
    ProteinModelPortaliP44859.
    SMRiP44859.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP44859.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni74 – 75Substrate bindingCombined sources1 Publication2
    Regioni208 – 209Substrate bindingCombined sources1 Publication2
    Regioni218 – 219Substrate bindingCombined sources1 Publication2

    Sequence similaritiesi

    Belongs to the diaminopimelate epimerase family.Curated

    Phylogenomic databases

    eggNOGiENOG4105E4Z. Bacteria.
    COG0253. LUCA.
    KOiK01778.
    OMAiMCGNGGR.
    PhylomeDBiP44859.

    Family and domain databases

    HAMAPiMF_00197. DAP_epimerase. 1 hit.
    InterProiView protein in InterPro
    IPR018510. DAP_epimerase_AS.
    IPR001653. DAP_epimerase_DapF.
    PANTHERiPTHR31689. PTHR31689. 1 hit.
    PfamiView protein in Pfam
    PF01678. DAP_epimerase. 2 hits.
    TIGRFAMsiTIGR00652. DapF. 1 hit.
    PROSITEiView protein in PROSITE
    PS01326. DAP_EPIMERASE. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P44859-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MQFSKMHGLG NDFVVVDGVT QNVFFTPETI RRLANRHCGI GFDQLLIVEA
    60 70 80 90 100
    PYDPELDFHY RIFNADGSEV SQCGNGARCF ARFVTLKGLT NKKDISVSTQ
    110 120 130 140 150
    KGNMVLTVKD DNQIRVNMGE PIWEPAKIPF TANKFEKNYI LRTDIQTVLC
    160 170 180 190 200
    GAVSMGNPHC VVQVDDIQTA NVEQLGPLLE SHERFPERVN AGFMQIINKE
    210 220 230 240 250
    HIKLRVYERG AGETQACGSG ACAAVAVGIM QGLLNNNVQV DLPGGSLMIE
    260 270
    WNGVGHPLYM TGEATHIYDG FITL
    Length:274
    Mass (Da):30,249
    Last modified:November 1, 1995 - v1
    Checksum:i321B3CDAFFE81EDA
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L42023 Genomic DNA. Translation: AAC22409.1.
    PIRiF64090.
    RefSeqiNP_438909.1. NC_000907.1.
    WP_005655521.1. NC_000907.1.

    Genome annotation databases

    EnsemblBacteriaiAAC22409; AAC22409; HI_0750.
    GeneIDi949560.
    KEGGihin:HI0750.
    PATRICifig|71421.8.peg.787.

    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.

    Entry informationi

    Entry nameiDAPF_HAEIN
    AccessioniPrimary (citable) accession number: P44859
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: November 1, 1995
    Last modified: June 7, 2017
    This is version 118 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Haemophilus influenzae
      Haemophilus influenzae (strain Rd): entries and gene names
    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