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Protein

4-hydroxy-tetrahydrodipicolinate reductase

Gene

dapB

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
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 (Probable). Uses NADPH as a reductant with much more efficiency than NADH.UniRule annotationCurated1 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 annotation

Enzyme regulationi

Is inhibited by high concentrations of NADH.1 Publication

Kineticsi

  1. KM=2.5 µM for NADH (at 30 degrees Celsius)1 Publication
  2. KM=0.6 µM for NADPH (at 30 degrees Celsius)1 Publication
  3. KM=1.8 µM for NADH (at 45 degrees Celsius)1 Publication
  4. KM=2.1 µM for NADPH (at 45 degrees Celsius)1 Publication

    Temperature dependencei

    Is stable for up to 48 hours at 80 degrees Celsius. Has a thermal denaturation midpoint (Tm) of 95.7 degrees Celsius.1 Publication

    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. no protein annotated in this organism
    2. no protein annotated in this organism
    3. Dihydrodipicolinate synthase (Tmari_1529), 4-hydroxy-tetrahydrodipicolinate synthase (dapA)
    4. 4-hydroxy-tetrahydrodipicolinate reductase (Tmari_1528), 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
    Active sitei127 – 1271Proton donor/acceptorUniRule annotation
    Binding sitei128 – 1281SubstrateUniRule annotation
    Active sitei131 – 1311Proton donorCurated

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi7 – 126NAD(P)UniRule annotation1 Publication
    Nucleotide bindingi71 – 733NAD(P)UniRule annotation1 Publication
    Nucleotide bindingi95 – 984NAD(P)UniRule annotation1 Publication

    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

    NAD, NADP

    Enzyme and pathway databases

    BRENDAi1.17.1.8. 6331.
    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:TM_1520
    OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
    Taxonomic identifieri243274 [NCBI]
    Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
    Proteomesi
    • UP000008183 Componenti: Chromosome

    Subcellular locationi

    • Cytoplasm UniRule annotation

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 2162164-hydroxy-tetrahydrodipicolinate reductasePRO_0000141502Add
    BLAST

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    STRINGi243274.TM1520.

    Structurei

    Secondary structure

    1
    216
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 65Combined sources
    Turni7 – 93Combined sources
    Helixi11 – 2212Combined sources
    Beta strandi26 – 327Combined sources
    Beta strandi35 – 384Combined sources
    Beta strandi43 – 475Combined sources
    Helixi51 – 533Combined sources
    Helixi54 – 6411Combined sources
    Beta strandi67 – 704Combined sources
    Helixi77 – 8610Combined sources
    Turni87 – 893Combined sources
    Beta strandi90 – 945Combined sources
    Helixi100 – 11516Combined sources
    Turni116 – 1183Combined sources
    Beta strandi119 – 1279Combined sources
    Helixi137 – 1459Combined sources
    Beta strandi152 – 1565Combined sources
    Beta strandi163 – 1697Combined sources
    Beta strandi171 – 18111Combined sources
    Helixi185 – 19814Combined sources
    Beta strandi203 – 2064Combined sources
    Helixi208 – 2125Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1VM6X-ray2.27A/B/C/D1-216[»]
    ProteinModelPortaliQ9X1K8.
    SMRiQ9X1K8. Positions 1-215.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9X1K8.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni137 – 1382Substrate bindingUniRule annotation

    Sequence similaritiesi

    Belongs to the DapB family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105DUK. Bacteria.
    COG0289. LUCA.
    InParanoidiQ9X1K8.
    KOiK00215.
    OMAiHNMSIGI.
    OrthoDBiEOG6SV5DS.

    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.
    SUPFAMiSSF51735. SSF51735. 2 hits.
    PROSITEiPS01298. DAPB. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9X1K8-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKYGIVGYSG RMGQEIQKVF SEKGHELVLK VDVNGVEELD SPDVVIDFSS
    60 70 80 90 100
    PEALPKTVDL CKKYRAGLVL GTTALKEEHL QMLRELSKEV PVVQAYNFSI
    110 120 130 140 150
    GINVLKRFLS ELVKVLEDWD VEIVETHHRF KKDAPSGTAI LLESALGKSV
    160 170 180 190 200
    PIHSLRVGGV PGDHVVVFGN IGETIEIKHR AISRTVFAIG ALKAAEFLVG
    210
    KDPGMYSFEE VIFGGE
    Length:216
    Mass (Da):23,731
    Last modified:November 1, 1999 - v1
    Checksum:i2C5670DF62C85528
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE000512 Genomic DNA. Translation: AAD36587.1.
    PIRiA72246.
    RefSeqiNP_229320.1. NC_000853.1.
    WP_004081877.1. NZ_CP011107.1.

    Genome annotation databases

    EnsemblBacteriaiAAD36587; AAD36587; TM_1520.
    GeneIDi897986.
    KEGGitma:TM1520.
    PATRICi23937998. VBITheMar51294_1537.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE000512 Genomic DNA. Translation: AAD36587.1.
    PIRiA72246.
    RefSeqiNP_229320.1. NC_000853.1.
    WP_004081877.1. NZ_CP011107.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1VM6X-ray2.27A/B/C/D1-216[»]
    ProteinModelPortaliQ9X1K8.
    SMRiQ9X1K8. Positions 1-215.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi243274.TM1520.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAD36587; AAD36587; TM_1520.
    GeneIDi897986.
    KEGGitma:TM1520.
    PATRICi23937998. VBITheMar51294_1537.

    Phylogenomic databases

    eggNOGiENOG4105DUK. Bacteria.
    COG0289. LUCA.
    InParanoidiQ9X1K8.
    KOiK00215.
    OMAiHNMSIGI.
    OrthoDBiEOG6SV5DS.

    Enzyme and pathway databases

    UniPathwayiUPA00034; UER00018.
    BRENDAi1.17.1.8. 6331.

    Miscellaneous databases

    EvolutionaryTraceiQ9X1K8.

    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.
    SUPFAMiSSF51735. SSF51735. 2 hits.
    PROSITEiPS01298. DAPB. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
    2. "Characterization of dihydrodipicolinate reductase from Thermotoga maritima reveals evolution of substrate binding kinetics."
      Pearce F.G., Sprissler C., Gerrard J.A.
      J. Biochem. 143:617-623(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.27 ANGSTROMS) IN COMPLEX WITH NADH, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, ENZYME REGULATION, SUBUNIT.
      Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.

    Entry informationi

    Entry nameiDAPB_THEMA
    AccessioniPrimary (citable) accession number: Q9X1K8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: November 1, 1999
    Last modified: April 13, 2016
    This is version 122 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 in E.coli 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.Curated

    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.