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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

    Pathway: 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), Aspartate-semialdehyde dehydrogenase (asd)
    3. 4-hydroxy-tetrahydrodipicolinate synthase (dapA), 4-hydroxy-tetrahydrodipicolinate synthase (dapA)
    4. 4-hydroxy-tetrahydrodipicolinate reductase (dapB), 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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei38 – 381NADUniRule annotation1 Publication
    Binding sitei39 – 391NADPUniRule annotation2 Publications
    Active sitei159 – 1591Proton donor/acceptor
    Binding sitei160 – 1601Substrate
    Active sitei163 – 1631Proton donor

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi12 – 176NAD(P)UniRule annotation1 Publication
    Nucleotide bindingi102 – 1043NAD(P)UniRule annotation1 Publication
    Nucleotide bindingi126 – 1294NAD(P)UniRule annotation1 Publication

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 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)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi159 – 1591H → A or Q: 135 to 200-fold reduction in catalytic activity. 1 Publication
    Mutagenesisi163 – 1631K → A, C or Q: 625 to 830-fold reduction in catalytic activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 2732734-hydroxy-tetrahydrodipicolinate reductasePRO_0000141437Add
    BLAST

    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

    Protein-protein interaction databases

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

    Structurei

    Secondary structure

    1
    273
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 106Combined sources
    Turni11 – 144Combined sources
    Helixi16 – 2712Combined sources
    Beta strandi32 – 376Combined sources
    Turni44 – 474Combined sources
    Beta strandi52 – 565Combined sources
    Beta strandi62 – 643Combined sources
    Turni67 – 715Combined sources
    Beta strandi74 – 785Combined sources
    Helixi82 – 9413Combined sources
    Beta strandi98 – 1014Combined sources
    Helixi108 – 11710Combined sources
    Turni118 – 1203Combined sources
    Beta strandi123 – 1253Combined sources
    Helixi131 – 14717Combined sources
    Turni148 – 1503Combined sources
    Beta strandi151 – 1599Combined sources
    Beta strandi165 – 1673Combined sources
    Helixi169 – 18113Combined sources
    Helixi186 – 1883Combined sources
    Beta strandi206 – 2127Combined sources
    Beta strandi218 – 2269Combined sources
    Beta strandi229 – 2379Combined sources
    Helixi241 – 25414Combined sources
    Beta strandi259 – 2624Combined sources
    Helixi264 – 2674Combined sources
    Helixi270 – 2723Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 2-273.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP04036.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni169 – 1702Substrate binding

    Sequence similaritiesi

    Belongs to the DapB family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0289.
    HOGENOMiHOG000227153.
    InParanoidiP04036.
    KOiK00215.
    OMAiCAVYARE.
    OrthoDBiEOG6SV5DS.
    PhylomeDBiP04036.

    Family and domain databases

    Gene3Di3.40.50.720. 1 hit.
    HAMAPiMF_00102. DapB.
    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.
    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.

    Genome annotation databases

    EnsemblBacteriaiAAC73142; AAC73142; b0031.
    BAB96600; BAB96600; BAB96600.
    GeneIDi944762.
    KEGGiecj:Y75_p0031.
    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.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 2-273.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

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

    Chemistry

    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:Y75_p0031.
    eco:b0031.
    PATRICi32115153. VBIEscCol129921_0028.

    Organism-specific databases

    EchoBASEiEB0202.
    EcoGeneiEG10206. dapB.

    Phylogenomic databases

    eggNOGiCOG0289.
    HOGENOMiHOG000227153.
    InParanoidiP04036.
    KOiK00215.
    OMAiCAVYARE.
    OrthoDBiEOG6SV5DS.
    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.
    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.
    TIGRFAMsiTIGR00036. dapB. 1 hit.
    PROSITEiPS01298. DAPB. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Nucleotide sequence and expression of the Escherichia coli dapB gene."
      Bouvier J., Richaud C., Richaud F., Patte J.-C., Stragier P.
      J. Biol. Chem. 259:14829-14834(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region."
      Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A.
      Nucleic Acids Res. 20:3305-3308(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "Multiple regulatory signals in the control region of the Escherichia coli carAB operon."
      Bouvier J., Patte J.-C., Stragier P.
      Proc. Natl. Acad. Sci. U.S.A. 81:4139-4143(1984) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 269-273.
    6. "Expression, purification, and characterization of Escherichia coli dihydrodipicolinate reductase."
      Reddy S.G., Sacchettini J.C., Blanchard J.S.
      Biochemistry 34:3492-3501(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-18, FUNCTION, KINETIC PARAMETERS, SUBSTRATE SPECIFICITY, SUBUNIT, MASS SPECTROMETRY.
      Strain: K12.
    7. "Lysine represses transcription of the Escherichia coli dapB gene by preventing its activation by the ArgP activator."
      Bouvier J., Stragier P., Morales V., Remy E., Gutierrez C.
      J. Bacteriol. 190:5224-5229(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
      Strain: K12 / MG1655 / ATCC 47076.
    8. "NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase."
      Devenish S.R., Blunt J.W., Gerrard J.A.
      J. Med. Chem. 53:4808-4812(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, IDENTIFICATION OF HTPA AS REACTION SUBSTRTATE, ACTIVE SITE.
    9. "Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase."
      Scapin G., Blanchard J.S., Sacchettini J.C.
      Biochemistry 34:3502-3512(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH NADPH.
      Strain: K12.
    10. "Interaction of pyridine nucleotide substrates with Escherichia coli dihydrodipicolinate reductase: thermodynamic and structural analysis of binary complexes."
      Reddy S.G., Scapin G., Blanchard J.S.
      Biochemistry 35:13294-13302(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH NAD OR NUCLEOTIDE SUBSTRATE ANALOGS.
      Strain: K12.
    11. "Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase in complex with NADH and the inhibitor 2,6-pyridinedicarboxylate."
      Scapin G., Reddy S.G., Zheng R., Blanchard J.S.
      Biochemistry 36:15081-15088(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEX WITH NAD AND A SUBSTRATE ANALOG INHIBITOR, ENZYME REGULATION, KINETIC PARAMETERS, REACTION MECHANISM, ACTIVE SITE, SITE, MUTAGENESIS OF HIS-159 AND LYS-163.
      Strain: K12.

    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: June 24, 2015
    This is version 148 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

    External Data

    Dasty 3

    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 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.