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Protein

4-hydroxy-tetrahydrodipicolinate reductase

Gene

dapB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. Can use both NADH and NADPH as a reductant, with NADH being twice as effective as NADPH.UniRule annotation2 Publications

Caution

Was originally thought to be a dihydrodipicolinate reductase (DHDPR), catalyzing the conversion of dihydrodipicolinate to tetrahydrodipicolinate. However, it was shown that the substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP) but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid (HTPA), the product released by the DapA-catalyzed reaction (PubMed:20503968).1 Publication

Catalytic activityi

(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H.UniRule annotation1 Publication

Enzyme regulationi

Is inhibited by 2,6-pyridine dicarboxylate (2,6-PDC or picolinate).1 Publication

Kineticsi

  1. KM=1.6 µM for NADH2 Publications
  2. KM=8 µM for NADPH2 Publications

    Pathwayi: L-lysine biosynthesis via DAP pathway

    This protein is involved in step 4 of the subpathway that synthesizes (S)-tetrahydrodipicolinate from L-aspartate.UniRule annotation
    Proteins known to be involved in the 4 steps of the subpathway in this organism are:
    1. Lysine-sensitive aspartokinase 3 (lysC), Bifunctional aspartokinase/homoserine dehydrogenase 1 (thrA), Bifunctional aspartokinase/homoserine dehydrogenase 2 (metL)
    2. Aspartate-semialdehyde dehydrogenase (asd)
    3. 4-hydroxy-tetrahydrodipicolinate synthase (dapA)
    4. 4-hydroxy-tetrahydrodipicolinate reductase (dapB)
    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 (S)-tetrahydrodipicolinate from L-aspartate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei38NADUniRule annotation1 Publication1
    Binding sitei39NADPUniRule annotation2 Publications1
    Active sitei159Proton donor/acceptor1
    Binding sitei160Substrate1
    Active sitei163Proton donor1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi12 – 17NAD(P)UniRule annotation1 Publication6
    Nucleotide bindingi102 – 104NAD(P)UniRule annotation1 Publication3
    Nucleotide bindingi126 – 129NAD(P)UniRule annotation1 Publication4

    GO - Molecular functioni

    • 4-hydroxy-tetrahydrodipicolinate reductase Source: EcoCyc
    • identical protein binding Source: EcoCyc

    GO - Biological processi

    • cellular amino acid biosynthetic process Source: EcoliWiki
    • diaminopimelate biosynthetic process Source: EcoliWiki
    • lysine biosynthetic process via diaminopimelate Source: UniProtKB-UniPathway

    Keywordsi

    Molecular functionOxidoreductase
    Biological processAmino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis
    LigandNAD, NADP

    Enzyme and pathway databases

    BioCyciEcoCyc:DIHYDROPICRED-MONOMER
    MetaCyc:DIHYDROPICRED-MONOMER
    BRENDAi1.17.1.8 2026
    UniPathwayiUPA00034; UER00018

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    4-hydroxy-tetrahydrodipicolinate reductaseUniRule annotation (EC:1.17.1.8UniRule annotation)
    Short name:
    HTPA reductaseUniRule annotation
    Gene namesi
    Name:dapBUniRule annotation
    Ordered Locus Names:b0031, JW0029
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10206 dapB

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi159H → A or Q: 135 to 200-fold reduction in catalytic activity. 1 Publication1
    Mutagenesisi163K → A, C or Q: 625 to 830-fold reduction in catalytic activity. 1 Publication1

    Chemistry databases

    DrugBankiDB03969 3-Acetyl Pyridine Adenine Dinucleotide
    DB04267 Dipicolinic Acid

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001414371 – 2734-hydroxy-tetrahydrodipicolinate reductaseAdd BLAST273

    Proteomic databases

    PaxDbiP04036
    PRIDEiP04036

    2D gel databases

    SWISS-2DPAGEiP04036

    Expressioni

    Inductioni

    Expression of dapB is up-regulated by ArgP and is repressed by lysine that prevents the binding of the ArgP activator. Thus, ArgP contributes to enhanced transcription of dapB when lysine becomes limiting.1 Publication

    Interactioni

    Subunit structurei

    Homotetramer.UniRule annotation4 Publications

    GO - Molecular functioni

    • identical protein binding Source: EcoCyc

    Protein-protein interaction databases

    BioGridi4261490, 16 interactors
    DIPiDIP-9399N
    IntActiP04036, 1 interactor
    STRINGi316385.ECDH10B_0032

    Chemistry databases

    BindingDBiP04036

    Structurei

    Secondary structure

    1273
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi5 – 10Combined sources6
    Turni11 – 14Combined sources4
    Helixi16 – 27Combined sources12
    Beta strandi32 – 37Combined sources6
    Turni44 – 47Combined sources4
    Beta strandi52 – 56Combined sources5
    Beta strandi62 – 64Combined sources3
    Turni67 – 71Combined sources5
    Beta strandi74 – 78Combined sources5
    Helixi82 – 94Combined sources13
    Beta strandi98 – 101Combined sources4
    Helixi108 – 117Combined sources10
    Turni118 – 120Combined sources3
    Beta strandi123 – 125Combined sources3
    Helixi131 – 147Combined sources17
    Turni148 – 150Combined sources3
    Beta strandi151 – 159Combined sources9
    Beta strandi165 – 167Combined sources3
    Helixi169 – 181Combined sources13
    Helixi186 – 188Combined sources3
    Beta strandi206 – 212Combined sources7
    Beta strandi218 – 226Combined sources9
    Beta strandi229 – 237Combined sources9
    Helixi241 – 254Combined sources14
    Beta strandi259 – 262Combined sources4
    Helixi264 – 267Combined sources4
    Helixi270 – 272Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1ARZX-ray2.60A/B/C/D1-273[»]
    1DIHX-ray2.20A1-273[»]
    1DRUX-ray2.20A1-273[»]
    1DRVX-ray2.20A1-273[»]
    1DRWX-ray2.20A1-273[»]
    ProteinModelPortaliP04036
    SMRiP04036
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP04036

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni169 – 170Substrate binding2

    Sequence similaritiesi

    Belongs to the DapB family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105DUK Bacteria
    COG0289 LUCA
    HOGENOMiHOG000227153
    InParanoidiP04036
    KOiK00215
    OMAiRESFMPG
    PhylomeDBiP04036

    Family and domain databases

    HAMAPiMF_00102 DapB, 1 hit
    InterProiView protein in InterPro
    IPR022663 DapB_C
    IPR000846 DapB_N
    IPR022664 DapB_N_CS
    IPR023940 DHDPR_bac
    IPR036291 NAD(P)-bd_dom_sf
    PANTHERiPTHR20836 PTHR20836, 1 hit
    PfamiView protein in Pfam
    PF05173 DapB_C, 1 hit
    PF01113 DapB_N, 1 hit
    PIRSFiPIRSF000161 DHPR, 1 hit
    SUPFAMiSSF51735 SSF51735, 2 hits
    TIGRFAMsiTIGR00036 dapB, 1 hit
    PROSITEiView protein in PROSITE
    PS01298 DAPB, 1 hit

    Sequencei

    Sequence statusi: Complete.

    P04036-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MHDANIRVAI AGAGGRMGRQ LIQAALALEG VQLGAALERE GSSLLGSDAG
    60 70 80 90 100
    ELAGAGKTGV TVQSSLDAVK DDFDVFIDFT RPEGTLNHLA FCRQHGKGMV
    110 120 130 140 150
    IGTTGFDEAG KQAIRDAAAD IAIVFAANFS VGVNVMLKLL EKAAKVMGDY
    160 170 180 190 200
    TDIEIIEAHH RHKVDAPSGT ALAMGEAIAH ALDKDLKDCA VYSREGHTGE
    210 220 230 240 250
    RVPGTIGFAT VRAGDIVGEH TAMFADIGER LEITHKASSR MTFANGAVRS
    260 270
    ALWLSGKESG LFDMRDVLDL NNL
    Length:273
    Mass (Da):28,757
    Last modified:November 1, 1986 - v1
    Checksum:i0ADE6837A6CF932C
    GO

    Mass spectrometryi

    Molecular mass is 28758±8 Da from positions 1 - 273. Determined by ESI. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M10611 Genomic DNA Translation: AAA23666.1
    U00096 Genomic DNA Translation: AAC73142.1
    AP009048 Genomic DNA Translation: BAB96600.1
    J01597 Genomic DNA No translation available.
    PIRiA00375 RDECPD
    RefSeqiNP_414572.1, NC_000913.3
    WP_000543604.1, NZ_LN832404.1

    Genome annotation databases

    EnsemblBacteriaiAAC73142; AAC73142; b0031
    BAB96600; BAB96600; BAB96600
    GeneIDi944762
    KEGGiecj:JW0029
    eco:b0031
    PATRICifig|1411691.4.peg.2254

    Similar proteinsi

    Entry informationi

    Entry nameiDAPB_ECOLI
    AccessioniPrimary (citable) accession number: P04036
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1986
    Last sequence update: November 1, 1986
    Last modified: March 28, 2018
    This is version 162 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, Direct protein sequencing, Reference proteome

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