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Protein

Meso-diaminopimelate D-dehydrogenase

Gene

ddh

Organism
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the reversible NADPH-dependent reductive amination of L-2-amino-6-oxopimelate, the acyclic form of L-tetrahydrodipicolinate, to generate the meso compound, D,L-2,6-diaminopimelate. Probably plays a role in lysine biosynthesis. Exhibits a high substrate specificity for meso-2,6-diaminopimelate, since L,L-2,6-diaminopimelate, D,D-2,6-diaminopimelate, L-glutamate, L-alanine, L-leucine, L-valine, L-aspartate, L-threonine, L-homoserine, L-methionine, L-lysine, L-serine, L-phenylalanine, L-tyrosine, L-tryptophan, L-ornithine, L-histidine, L-arginine, D-glutamate, and D-alanine are not substrates for the oxidative deamination reaction. Can use NAD+ only poorly since the activity observed in the presence of NAD+ is about 3% of that with NADP+.2 Publications

Catalytic activityi

Meso-2,6-diaminoheptanedioate + H2O + NADP+ = L-2-amino-6-oxoheptanedioate + NH3 + NADPH.2 Publications

Activity regulationi

L,L-2,6-diaminopimelate and D,D-2,6-diaminopimelate competitively inhibit the oxidative deamination of meso-2,6-diaminopimelate. The enzyme is also inhibited by L-cysteine, and by p-chloromercuribenzoate, iodoacetic acid and HgCl2 in vitro.1 Publication

Kineticsi

  1. KM=3.1 mM for meso-2,6-diaminoheptanedioate1 Publication
  2. KM=0.12 mM for NADP+1 Publication
  3. KM=0.13 mM for NADPH1 Publication
  4. KM=0.28 mM for L-2-amino-6-oxoheptanedioate1 Publication
  5. KM=36 mM for ammonia1 Publication

    pH dependencei

    Optimum pH is about 9.8 for the oxidative deamination of meso-diaminopimelate and 7.9 for the reductive amination of L-2-amino-6-oxopimelate.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 (S)-tetrahydrodipicolinate.
    Proteins known to be involved in this subpathway in this organism are:
    1. Meso-diaminopimelate D-dehydrogenase (ddh)
    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 (S)-tetrahydrodipicolinate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei90Substrate1
    Binding sitei120Substrate; via carbonyl oxygen1
    Binding sitei144Substrate1
    Binding sitei169Substrate1
    Binding sitei195Substrate1
    Binding sitei244Substrate1
    Binding sitei270Substrate1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi11 – 14NADP4
    Nucleotide bindingi35 – 37NADP3
    Nucleotide bindingi65 – 68NADP4
    Nucleotide bindingi88 – 90NADP3
    Nucleotide bindingi117 – 121NADP5

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

    Molecular functionOxidoreductase
    Biological processAmino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis
    LigandNADP

    Enzyme and pathway databases

    BioCyciCORYNE:G18NG-12233-MONOMER
    MetaCyc:MONOMER-6621
    BRENDAi1.4.1.16 960
    UniPathwayi
    UPA00034;UER00026

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Meso-diaminopimelate D-dehydrogenase (EC:1.4.1.16)
    Short name:
    DAPDH
    Short name:
    Meso-DAP dehydrogenase
    Gene namesi
    Name:ddh
    Ordered Locus Names:Cgl2617, cg2900
    OrganismiCorynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
    Taxonomic identifieri196627 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesCorynebacteriaceaeCorynebacterium
    Proteomesi
    • UP000000582 Componenti: Chromosome

    Pathology & Biotechi

    Chemistry databases

    DrugBankiDB02892 L-2-Amino-6-Methylene-Pimelic Acid

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000798481 – 320Meso-diaminopimelate D-dehydrogenaseAdd BLAST320

    2D gel databases

    World-2DPAGEi0001:P04964

    Interactioni

    Subunit structurei

    Homodimer.5 Publications

    Protein-protein interaction databases

    STRINGi196627.cg2900

    Structurei

    Secondary structure

    1320
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    ProteinModelPortaliP04964
    SMRiP04964
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP04964

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni150 – 151Substrate binding2

    Domaini

    Is composed of three domains: a dinucleotide binding domain, a dimerization domain, and a substrate-binding domain.1 Publication

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4105DGA Bacteria
    ENOG410XPX2 LUCA
    HOGENOMiHOG000059861
    KOiK03340
    OMAiDSFDTHA

    Family and domain databases

    InterProiView protein in InterPro
    IPR032094 DAPDH_C
    IPR010190 Diaminopimelate_DH_Ddh
    IPR036291 NAD(P)-bd_dom_sf
    PfamiView protein in Pfam
    PF16654 DAPDH_C, 1 hit
    PIRSFiPIRSF025648 DDH, 1 hit
    SUPFAMiSSF51735 SSF51735, 1 hit
    TIGRFAMsiTIGR01921 DAP-DH, 1 hit

    Sequencei

    Sequence statusi: Complete.

    P04964-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MTNIRVAIVG YGNLGRSVEK LIAKQPDMDL VGIFSRRATL DTKTPVFDVA
    60 70 80 90 100
    DVDKHADDVD VLFLCMGSAT DIPEQAPKFA QFACTVDTYD NHRDIPRHRQ
    110 120 130 140 150
    VMNEAATAAG NVALVSTGWD PGMFSINRVY AAAVLAEHQQ HTFWGPGLSQ
    160 170 180 190 200
    GHSDALRRIP GVQKAVQYTL PSEDALEKAR RGEAGDLTGK QTHKRQCFVV
    210 220 230 240 250
    ADAADHERIE NDIRTMPDYF VGYEVEVNFI DEATFDSEHT GMPHGGHVIT
    260 270 280 290 300
    TGDTGGFNHT VEYILKLDRN PDFTASSQIA FGRAAHRMKQ QGQSGAFTVL
    310 320
    EVAPYLLSPE NLDDLIARDV
    Length:320
    Mass (Da):35,199
    Last modified:August 13, 1987 - v1
    Checksum:iD29D3EB6DFDA35DE
    GO

    Mass spectrometryi

    Molecular mass is 35198 Da from positions 1 - 320. Determined by ESI. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Y00151 Genomic DNA Translation: CAA68346.1
    BA000036 Genomic DNA Translation: BAC00011.1
    BX927155 Genomic DNA Translation: CAF21279.1
    PIRiS07384
    RefSeqiNP_601818.2, NC_003450.3
    WP_011015254.1, NC_006958.1

    Genome annotation databases

    EnsemblBacteriaiBAC00011; BAC00011; BAC00011
    CAF21279; CAF21279; cg2900
    GeneIDi1020564
    KEGGicgb:cg2900
    cgl:NCgl2528
    PATRICifig|196627.13.peg.2553

    Similar proteinsi

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Y00151 Genomic DNA Translation: CAA68346.1
    BA000036 Genomic DNA Translation: BAC00011.1
    BX927155 Genomic DNA Translation: CAF21279.1
    PIRiS07384
    RefSeqiNP_601818.2, NC_003450.3
    WP_011015254.1, NC_006958.1

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1DAPX-ray2.20A/B1-320[»]
    1F06X-ray2.10A/B1-320[»]
    2DAPX-ray2.20A1-320[»]
    3DAPX-ray2.20A/B1-320[»]
    5LOAX-ray1.84A/B2-320[»]
    5LOCX-ray2.04A/B2-320[»]
    ProteinModelPortaliP04964
    SMRiP04964
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi196627.cg2900

    Chemistry databases

    DrugBankiDB02892 L-2-Amino-6-Methylene-Pimelic Acid

    2D gel databases

    World-2DPAGEi0001:P04964

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAC00011; BAC00011; BAC00011
    CAF21279; CAF21279; cg2900
    GeneIDi1020564
    KEGGicgb:cg2900
    cgl:NCgl2528
    PATRICifig|196627.13.peg.2553

    Phylogenomic databases

    eggNOGiENOG4105DGA Bacteria
    ENOG410XPX2 LUCA
    HOGENOMiHOG000059861
    KOiK03340
    OMAiDSFDTHA

    Enzyme and pathway databases

    UniPathwayi
    UPA00034;UER00026

    BioCyciCORYNE:G18NG-12233-MONOMER
    MetaCyc:MONOMER-6621
    BRENDAi1.4.1.16 960

    Miscellaneous databases

    EvolutionaryTraceiP04964

    Family and domain databases

    InterProiView protein in InterPro
    IPR032094 DAPDH_C
    IPR010190 Diaminopimelate_DH_Ddh
    IPR036291 NAD(P)-bd_dom_sf
    PfamiView protein in Pfam
    PF16654 DAPDH_C, 1 hit
    PIRSFiPIRSF025648 DDH, 1 hit
    SUPFAMiSSF51735 SSF51735, 1 hit
    TIGRFAMsiTIGR01921 DAP-DH, 1 hit
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDAPDH_CORGL
    AccessioniPrimary (citable) accession number: P04964
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 13, 1987
    Last sequence update: August 13, 1987
    Last modified: September 12, 2018
    This is version 135 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. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health

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