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Protein

4-hydroxy-tetrahydrodipicolinate reductase

Gene

dapB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

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

    GO - Biological processi

    • cellular amino acid biosynthetic process Source: EcoliWiki
    • diaminopimelate biosynthetic process Source: EcoliWiki
    • lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Amino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis

    Keywords - Ligandi

    NAD, NADP

    Enzyme and pathway databases

    BioCyciEcoCyc:DIHYDROPICRED-MONOMER.
    ECOL316407:JW0029-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: UniProtKB
    Complete GO annotation...

    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

    PTM / Processingi

    Molecule processing

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

    Proteomic databases

    PaxDbiP04036.
    PRIDEiP04036.

    2D gel databases

    SWISS-2DPAGEP04036.

    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

    DIPiDIP-9399N.
    IntActiP04036. 1 interactor.
    STRINGi511145.b0031.

    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.
    OMAiYAREGHT.
    PhylomeDBiP04036.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    HAMAPiMF_00102. DapB. 1 hit.
    InterProiIPR022663. DapB_C.
    IPR000846. DapB_N.
    IPR022664. DapB_N_CS.
    IPR023940. DHDPR_bac.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PANTHERiPTHR20836. PTHR20836. 1 hit.
    PfamiPF05173. DapB_C. 1 hit.
    PF01113. DapB_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000161. DHPR. 1 hit.
    SUPFAMiSSF51735. SSF51735. 2 hits.
    TIGRFAMsiTIGR00036. dapB. 1 hit.
    PROSITEiPS01298. DAPB. 1 hit.
    [Graphical view]

    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.
    PATRICi32115153. VBIEscCol129921_0028.

    Cross-referencesi

    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.

    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...

    Protein-protein interaction databases

    DIPiDIP-9399N.
    IntActiP04036. 1 interactor.
    STRINGi511145.b0031.

    Chemistry databases

    BindingDBiP04036.

    2D gel databases

    SWISS-2DPAGEP04036.

    Proteomic databases

    PaxDbiP04036.
    PRIDEiP04036.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73142; AAC73142; b0031.
    BAB96600; BAB96600; BAB96600.
    GeneIDi944762.
    KEGGiecj:JW0029.
    eco:b0031.
    PATRICi32115153. VBIEscCol129921_0028.

    Organism-specific databases

    EchoBASEiEB0202.
    EcoGeneiEG10206. dapB.

    Phylogenomic databases

    eggNOGiENOG4105DUK. Bacteria.
    COG0289. LUCA.
    HOGENOMiHOG000227153.
    InParanoidiP04036.
    KOiK00215.
    OMAiYAREGHT.
    PhylomeDBiP04036.

    Enzyme and pathway databases

    UniPathwayiUPA00034; UER00018.
    BioCyciEcoCyc:DIHYDROPICRED-MONOMER.
    ECOL316407:JW0029-MONOMER.
    MetaCyc:DIHYDROPICRED-MONOMER.
    BRENDAi1.17.1.8. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP04036.
    PROiP04036.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    HAMAPiMF_00102. DapB. 1 hit.
    InterProiIPR022663. DapB_C.
    IPR000846. DapB_N.
    IPR022664. DapB_N_CS.
    IPR023940. DHDPR_bac.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view]
    PANTHERiPTHR20836. PTHR20836. 1 hit.
    PfamiPF05173. DapB_C. 1 hit.
    PF01113. DapB_N. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000161. DHPR. 1 hit.
    SUPFAMiSSF51735. SSF51735. 2 hits.
    TIGRFAMsiTIGR00036. dapB. 1 hit.
    PROSITEiPS01298. DAPB. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDAPB_ECOLI
    AccessioniPrimary (citable) accession number: P04036
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1986
    Last sequence update: November 1, 1986
    Last modified: November 2, 2016
    This is version 154 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    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

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    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

    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.