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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: Annotation score: 5 out of 5-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

Enzyme 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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei90 – 901Substrate
    Binding sitei120 – 1201Substrate; via carbonyl oxygen
    Binding sitei144 – 1441Substrate
    Binding sitei169 – 1691Substrate
    Binding sitei195 – 1951Substrate
    Binding sitei244 – 2441Substrate
    Binding sitei270 – 2701Substrate

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi11 – 144NADP
    Nucleotide bindingi35 – 373NADP
    Nucleotide bindingi65 – 684NADP
    Nucleotide bindingi88 – 903NADP
    Nucleotide bindingi117 – 1215NADP

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Amino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis

    Keywords - Ligandi

    NADP

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-6621.
    BRENDAi1.4.1.16. 960.
    UniPathwayiUPA00034; 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

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 320320Meso-diaminopimelate D-dehydrogenasePRO_0000079848Add
    BLAST

    2D gel databases

    World-2DPAGE0001:P04964.

    Interactioni

    Subunit structurei

    Homodimer.5 Publications

    Protein-protein interaction databases

    STRINGi196627.cg2900.

    Structurei

    Secondary structure

    1
    320
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 96Combined sources
    Helixi13 – 2210Combined sources
    Beta strandi28 – 3811Combined sources
    Beta strandi41 – 444Combined sources
    Beta strandi46 – 483Combined sources
    Helixi49 – 546Combined sources
    Turni55 – 584Combined sources
    Beta strandi60 – 645Combined sources
    Turni68 – 703Combined sources
    Helixi71 – 799Combined sources
    Turni80 – 823Combined sources
    Beta strandi83 – 864Combined sources
    Helixi92 – 943Combined sources
    Helixi95 – 10915Combined sources
    Beta strandi112 – 1143Combined sources
    Turni119 – 1224Combined sources
    Helixi123 – 13412Combined sources
    Beta strandi136 – 1449Combined sources
    Beta strandi146 – 1483Combined sources
    Helixi150 – 1578Combined sources
    Beta strandi163 – 1719Combined sources
    Helixi173 – 1819Combined sources
    Helixi189 – 1924Combined sources
    Beta strandi193 – 2008Combined sources
    Helixi203 – 2053Combined sources
    Helixi206 – 2149Combined sources
    Turni217 – 2226Combined sources
    Beta strandi223 – 2297Combined sources
    Helixi232 – 2387Combined sources
    Beta strandi239 – 2424Combined sources
    Beta strandi244 – 25613Combined sources
    Beta strandi258 – 26811Combined sources
    Helixi270 – 29021Combined sources
    Beta strandi295 – 2973Combined sources
    Helixi299 – 3013Combined sources
    Helixi304 – 3074Combined sources
    Helixi312 – 3198Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DAPX-ray2.20A/B1-320[»]
    1F06X-ray2.10A/B1-320[»]
    2DAPX-ray2.20A1-320[»]
    3DAPX-ray2.20A/B1-320[»]
    ProteinModelPortaliP04964.
    SMRiP04964. Positions 1-320.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP04964.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni150 – 1512Substrate binding

    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.
    OrthoDBiEOG6R87CG.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR032094. DAPDH_C.
    IPR010190. Diaminopimelate_DH_Ddh.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF16654. DAPDH_C. 1 hit.
    [Graphical view]
    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.
    PATRICi21497280. VBICorGlu203724_2553.

    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
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1DAPX-ray2.20A/B1-320[»]
    1F06X-ray2.10A/B1-320[»]
    2DAPX-ray2.20A1-320[»]
    3DAPX-ray2.20A/B1-320[»]
    ProteinModelPortaliP04964.
    SMRiP04964. Positions 1-320.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi196627.cg2900.

    2D gel databases

    World-2DPAGE0001:P04964.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAC00011; BAC00011; BAC00011.
    CAF21279; CAF21279; cg2900.
    GeneIDi1020564.
    KEGGicgb:cg2900.
    cgl:NCgl2528.
    PATRICi21497280. VBICorGlu203724_2553.

    Phylogenomic databases

    eggNOGiENOG4105DGA. Bacteria.
    ENOG410XPX2. LUCA.
    HOGENOMiHOG000059861.
    KOiK03340.
    OMAiDSFDTHA.
    OrthoDBiEOG6R87CG.

    Enzyme and pathway databases

    UniPathwayiUPA00034; UER00026.
    BioCyciMetaCyc:MONOMER-6621.
    BRENDAi1.4.1.16. 960.

    Miscellaneous databases

    EvolutionaryTraceiP04964.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    InterProiIPR032094. DAPDH_C.
    IPR010190. Diaminopimelate_DH_Ddh.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PfamiPF16654. DAPDH_C. 1 hit.
    [Graphical view]
    PIRSFiPIRSF025648. DDH. 1 hit.
    SUPFAMiSSF51735. SSF51735. 1 hit.
    TIGRFAMsiTIGR01921. DAP-DH. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Nucleotide sequence of the meso-diaminopimelate D-dehydrogenase gene from Corynebacterium glutamicum."
      Ishino S., Mizukami T., Yamaguchi K., Katsumata R., Araki K.
      Nucleic Acids Res. 15:3917-3917(1987) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: KY 10755.
    2. "The Corynebacterium glutamicum genome: features and impacts on biotechnological processes."
      Ikeda M., Nakagawa S.
      Appl. Microbiol. Biotechnol. 62:99-109(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
    4. "Characterization of meso-diaminopimelate dehydrogenase from Corynebacterium glutamicum."
      Misono H., Ogasawara M., Nagasaki S.
      Agric. Biol. Chem. 50:2729-2734(1986)
      Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBUNIT.
      Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
    5. "Expression, purification, and crystallization of meso-diaminopimelate dehydrogenase from Corynebacterium glutamicum."
      Reddy S.G., Scapin G., Blanchard J.S.
      Proteins 25:514-516(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, CRYSTALLIZATION, MASS SPECTROMETRY, SUBUNIT.
      Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
    6. "Three-dimensional structure of meso-diaminopimelic acid dehydrogenase from Corynebacterium glutamicum."
      Scapin G., Reddy S.G., Blanchard J.S.
      Biochemistry 35:13540-13551(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH NADP(+), DOMAIN, SUBUNIT.
      Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
    7. "Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase."
      Scapin G., Cirilli M., Reddy S.G., Gao Y., Vederas J.C., Blanchard J.S.
      Biochemistry 37:3278-3285(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEXES WITH MESO-2,6-DIAMINOPIMELATE; NADP(+) AND AN ISOXAZOLINE INHIBITOR, SUBUNIT.
      Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.
    8. "The three-dimensional structure of the ternary complex of Corynebacterium glutamicum diaminopimelate dehydrogenase-NADPH-L-2-amino-6-methylene-pimelate."
      Cirilli M., Scapin G., Sutherland A., Vederas J.C., Blanchard J.S.
      Protein Sci. 9:2034-2037(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH NADP(+) AND SUBSTRATE ANALOG INHIBITOR, SUBUNIT.
      Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025.

    Entry informationi

    Entry nameiDAPDH_CORGL
    AccessioniPrimary (citable) accession number: P04964
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 13, 1987
    Last sequence update: August 13, 1987
    Last modified: December 9, 2015
    This is version 125 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. 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

    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.