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P44859

- DAPF_HAEIN

UniProt

P44859 - DAPF_HAEIN

Protein

Diaminopimelate epimerase

Gene

dapF

Organism
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 104 (01 Oct 2014)
      Sequence version 1 (01 Nov 1995)
      Previous versions | rss
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    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.1 Publication

    Catalytic activityi

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

    Enzyme regulationi

    Inhibited by LL-aziridino (LL-AziDAP), DL-aziridino (DL-AziDAP), (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).2 Publications

    Kineticsi

    Kcat is 128 and 82 (sec-1) for L,L-DAP and D,L-DAP, respectively.

    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

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei11 – 111Substrate
    Binding sitei44 – 441Substrate
    Binding sitei64 – 641Substrate
    Active sitei73 – 731Proton donor/acceptor
    Binding sitei157 – 1571Substrate
    Sitei159 – 1591Important for catalytic activitySequence Analysis
    Binding sitei190 – 1901Substrate
    Sitei208 – 2081Important for catalytic activitySequence Analysis
    Active sitei217 – 2171Proton donor/acceptor

    GO - Molecular functioni

    1. diaminopimelate epimerase activity Source: UniProtKB-HAMAP

    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

    UniPathwayiUPA00034; UER00025.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Diaminopimelate epimerase (EC:5.1.1.7)
    Short name:
    DAP epimerase
    Alternative name(s):
    PLP-Independent Amino Acid Racemases
    Gene namesi
    Name:dapF
    Ordered Locus Names:HI_0750
    OrganismiHaemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
    Taxonomic identifieri71421 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPasteurellalesPasteurellaceaeHaemophilus
    ProteomesiUP000000579: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi73 – 731C → A: Inactive as epimerases, but it is able to rapidly catalyze the HF eliminatio 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. 2 Publications
    Mutagenesisi73 – 731C → S: 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 Publications
    Mutagenesisi217 – 2171C → A: Inactive as epimerases. It is able to rapidly catalyze the HF eliminatio 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. 2 Publications
    Mutagenesisi217 – 2171C → S: 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 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 274274Diaminopimelate epimerasePRO_0000149842Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi73 ↔ 2171 Publication

    Keywords - PTMi

    Disulfide bond

    Interactioni

    Subunit structurei

    Monomer.3 Publications

    Protein-protein interaction databases

    STRINGi71421.HI0750.

    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 strandi56 – 649
    Beta strandi69 – 713
    Helixi74 – 8613
    Beta strandi93 – 986
    Beta strandi103 – 1086
    Beta strandi114 – 1174
    Helixi125 – 1273
    Beta strandi137 – 1426
    Beta strandi147 – 16317
    Turni167 – 1693
    Helixi172 – 1809
    Beta strandi190 – 1989
    Beta strandi201 – 2088
    Turni209 – 2113
    Helixi218 – 23013
    Beta strandi236 – 2427
    Beta strandi245 – 2517
    Beta strandi258 – 2625
    Beta strandi265 – 2717

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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. Positions 1-274.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP44859.

    Family & Domainsi

    Region

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

    Sequence similaritiesi

    Belongs to the diaminopimelate epimerase family.Curated

    Phylogenomic databases

    eggNOGiCOG0253.
    KOiK01778.
    OMAiLIVEPPY.
    OrthoDBiEOG6ND0M5.
    PhylomeDBiP44859.

    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.

    P44859-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQFSKMHGLG NDFVVVDGVT QNVFFTPETI RRLANRHCGI GFDQLLIVEA    50
    PYDPELDFHY RIFNADGSEV SQCGNGARCF ARFVTLKGLT NKKDISVSTQ 100
    KGNMVLTVKD DNQIRVNMGE PIWEPAKIPF TANKFEKNYI LRTDIQTVLC 150
    GAVSMGNPHC VVQVDDIQTA NVEQLGPLLE SHERFPERVN AGFMQIINKE 200
    HIKLRVYERG AGETQACGSG ACAAVAVGIM QGLLNNNVQV DLPGGSLMIE 250
    WNGVGHPLYM TGEATHIYDG FITL 274
    Length:274
    Mass (Da):30,249
    Last modified:November 1, 1995 - v1
    Checksum:i321B3CDAFFE81EDA
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L42023 Genomic DNA. Translation: AAC22409.1.
    PIRiF64090.
    RefSeqiNP_438909.1. NC_000907.1.

    Genome annotation databases

    EnsemblBacteriaiAAC22409; AAC22409; HI_0750.
    GeneIDi949560.
    KEGGihin:HI0750.
    PATRICi20190143. VBIHaeInf48452_0787.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    L42023 Genomic DNA. Translation: AAC22409.1 .
    PIRi F64090.
    RefSeqi NP_438909.1. NC_000907.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1BWZ X-ray 2.72 A 1-274 [» ]
    1GQZ X-ray 1.75 A 1-274 [» ]
    2GKE X-ray 1.35 A 1-274 [» ]
    2GKJ X-ray 1.70 A 1-274 [» ]
    2Q9H X-ray 2.30 A 1-274 [» ]
    2Q9J X-ray 2.20 A 1-274 [» ]
    ProteinModelPortali P44859.
    SMRi P44859. Positions 1-274.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 71421.HI0750.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC22409 ; AAC22409 ; HI_0750 .
    GeneIDi 949560.
    KEGGi hin:HI0750.
    PATRICi 20190143. VBIHaeInf48452_0787.

    Phylogenomic databases

    eggNOGi COG0253.
    KOi K01778.
    OMAi LIVEPPY.
    OrthoDBi EOG6ND0M5.
    PhylomeDBi P44859.

    Enzyme and pathway databases

    UniPathwayi UPA00034 ; UER00025 .

    Miscellaneous databases

    EvolutionaryTracei P44859.

    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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 51907 / DSM 11121 / KW20 / Rd.
    2. "Chemical mechanism of Haemophilus influenzae diaminopimelate epimerase."
      Koo C.W., Blanchard J.S.
      Biochemistry 38:4416-4422(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, REACTION MECHANISM, BIOPHYSICOCHEMICAL PROPERTIES.
    3. "Identification of active site cysteine residues that function as general bases: diaminopimelate epimerase."
      Koo C.W., Sutherland A., Vederas J.C., Blanchard J.S.
      J. Am. Chem. Soc. 122:6122-6123(2000)
      Cited for: MUTAGENESIS OF CYS-73 AND CYS-217, ACTIVE SITE, ENZYME REGULATION.
    4. "Structural symmetry: the three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase."
      Cirilli M., Zheng R., Scapin G., Blanchard J.S.
      Biochemistry 37:16452-16458(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.72 ANGSTROMS), ACTIVE SITE, DISULFIDE BOND, SUBUNIT.
    5. "Refinement of Haemophilus influenzae diaminopimelic acid epimerase (DapF) at 1.75 A resolution suggests a mechanism for stereocontrol during catalysis."
      Lloyd A.J., Huyton T., Turkenburg J., Roper D.I.
      Acta Crystallogr. D 60:397-400(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS), REACTION MECHANISM.
    6. "Structural insights into stereochemical inversion by diaminopimelate epimerase: an antibacterial drug target."
      Pillai B., Cherney M.M., Diaper C.M., Sutherland A., Blanchard J.S., Vederas J.C., James M.N.
      Proc. Natl. Acad. Sci. U.S.A. 103:8668-8673(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.35 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, SUBSTRATE SPECIFICITY, ENZYME REGULATION.
    7. "Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase."
      Pillai B., Cherney M., Diaper C.M., Sutherland A., Blanchard J.S., Vederas J.C., James M.N.
      Biochem. Biophys. Res. Commun. 363:547-553(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF MUTANT SER-73 AND SER-217 IN COMPLEX WITH SUBSTRATE ANALOGS, MUTAGENESIS OF CYS-73 AND CYS-217.

    Entry informationi

    Entry nameiDAPF_HAEIN
    AccessioniPrimary (citable) accession number: P44859
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1995
    Last sequence update: November 1, 1995
    Last modified: October 1, 2014
    This is version 104 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. 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

    External Data

    Dasty 3