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P04036

- DAPB_ECOLI

UniProt

P04036 - DAPB_ECOLI

Protein

4-hydroxy-tetrahydrodipicolinate reductase

Gene

dapB

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 141 (01 Oct 2014)
      Sequence version 1 (01 Nov 1986)
      Previous versions | rss
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    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.2 PublicationsUniRule annotation

    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.1 PublicationUniRule annotation

    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

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei38 – 381NAD1 PublicationUniRule annotation
    Binding sitei39 – 391NADP2 PublicationsUniRule annotation
    Active sitei159 – 1591Proton donor/acceptor
    Binding sitei160 – 1601Substrate
    Active sitei163 – 1631Proton donor

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi12 – 176NAD(P)1 PublicationUniRule annotation
    Nucleotide bindingi102 – 1043NAD(P)1 PublicationUniRule annotation
    Nucleotide bindingi126 – 1294NAD(P)1 PublicationUniRule annotation

    GO - Molecular functioni

    1. 4-hydroxy-tetrahydrodipicolinate reductase Source: EcoCyc
    2. identical protein binding Source: EcoCyc
    3. NAD binding Source: UniProtKB-HAMAP
    4. NADPH binding Source: InterPro
    5. oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor Source: UniProtKB-HAMAP

    GO - Biological processi

    1. cellular amino acid biosynthetic process Source: EcoliWiki
    2. diaminopimelate biosynthetic process Source: EcoliWiki
    3. lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP

    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.
    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: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10206. dapB.

    Subcellular locationi

    GO - Cellular componenti

    1. cytosol Source: UniProtKB

    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

    Gene expression databases

    GenevestigatoriP04036.

    Interactioni

    Subunit structurei

    Homotetramer.4 PublicationsUniRule annotation

    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 – 106
    Turni11 – 144
    Helixi16 – 2712
    Beta strandi32 – 376
    Turni44 – 474
    Beta strandi52 – 565
    Beta strandi62 – 643
    Turni67 – 715
    Beta strandi74 – 785
    Helixi82 – 9413
    Beta strandi98 – 1014
    Helixi108 – 11710
    Turni118 – 1203
    Beta strandi123 – 1253
    Helixi131 – 14717
    Turni148 – 1503
    Beta strandi151 – 1599
    Beta strandi165 – 1673
    Helixi169 – 18113
    Helixi186 – 1883
    Beta strandi206 – 2127
    Beta strandi218 – 2269
    Beta strandi229 – 2379
    Helixi241 – 25414
    Beta strandi259 – 2624
    Helixi264 – 2674
    Helixi270 – 2723

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    KOiK00215.
    OMAiHTVWFAD.
    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.
    IPR011770. Dihydrodipicolinate_Rdtase.
    IPR023940. Dihydrodipicolinate_Rdtase_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

    MHDANIRVAI AGAGGRMGRQ LIQAALALEG VQLGAALERE GSSLLGSDAG    50
    ELAGAGKTGV TVQSSLDAVK DDFDVFIDFT RPEGTLNHLA FCRQHGKGMV 100
    IGTTGFDEAG KQAIRDAAAD IAIVFAANFS VGVNVMLKLL EKAAKVMGDY 150
    TDIEIIEAHH RHKVDAPSGT ALAMGEAIAH ALDKDLKDCA VYSREGHTGE 200
    RVPGTIGFAT VRAGDIVGEH TAMFADIGER LEITHKASSR MTFANGAVRS 250
    ALWLSGKESG LFDMRDVLDL NNL 273
    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:
    EMBL
    GenBank
    DDBJ
    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.
    YP_488337.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73142; AAC73142; b0031.
    BAB96600; BAB96600; BAB96600.
    GeneIDi12932496.
    944762.
    KEGGiecj:Y75_p0031.
    eco:b0031.
    PATRICi32115153. VBIEscCol129921_0028.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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.
    PIRi A00375. RDECPD.
    RefSeqi NP_414572.1. NC_000913.3.
    YP_488337.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1ARZ X-ray 2.60 A/B/C/D 1-273 [» ]
    1DIH X-ray 2.20 A 1-273 [» ]
    1DRU X-ray 2.20 A 1-273 [» ]
    1DRV X-ray 2.20 A 1-273 [» ]
    1DRW X-ray 2.20 A 1-273 [» ]
    ProteinModelPortali P04036.
    SMRi P04036. Positions 2-273.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-9399N.
    IntActi P04036. 1 interaction.
    STRINGi 511145.b0031.

    Chemistry

    BindingDBi P04036.

    2D gel databases

    SWISS-2DPAGE P04036.

    Proteomic databases

    PaxDbi P04036.
    PRIDEi P04036.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC73142 ; AAC73142 ; b0031 .
    BAB96600 ; BAB96600 ; BAB96600 .
    GeneIDi 12932496.
    944762.
    KEGGi ecj:Y75_p0031.
    eco:b0031.
    PATRICi 32115153. VBIEscCol129921_0028.

    Organism-specific databases

    EchoBASEi EB0202.
    EcoGenei EG10206. dapB.

    Phylogenomic databases

    eggNOGi COG0289.
    HOGENOMi HOG000227153.
    KOi K00215.
    OMAi HTVWFAD.
    OrthoDBi EOG6SV5DS.
    PhylomeDBi P04036.

    Enzyme and pathway databases

    UniPathwayi UPA00034 ; UER00018 .
    BioCyci EcoCyc:DIHYDROPICRED-MONOMER.
    ECOL316407:JW0029-MONOMER.
    MetaCyc:DIHYDROPICRED-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P04036.
    PROi P04036.

    Gene expression databases

    Genevestigatori P04036.

    Family and domain databases

    Gene3Di 3.40.50.720. 1 hit.
    HAMAPi MF_00102. DapB.
    InterProi IPR022663. DapB_C.
    IPR000846. DapB_N.
    IPR022664. DapB_N_CS.
    IPR011770. Dihydrodipicolinate_Rdtase.
    IPR023940. Dihydrodipicolinate_Rdtase_bac.
    IPR016040. NAD(P)-bd_dom.
    [Graphical view ]
    PANTHERi PTHR20836. PTHR20836. 1 hit.
    Pfami PF05173. DapB_C. 1 hit.
    PF01113. DapB_N. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000161. DHPR. 1 hit.
    TIGRFAMsi TIGR00036. dapB. 1 hit.
    PROSITEi PS01298. DAPB. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 141 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