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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. Aspartokinase (TM_1518)
    2. no protein annotated in this organism
    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)DescriptionActionsGraphical viewLength
    Active sitei127Proton donor/acceptorUniRule annotation1
    Binding sitei128SubstrateUniRule annotation1
    Active sitei131Proton donorCurated1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi7 – 12NAD(P)UniRule annotation1 Publication6
    Nucleotide bindingi71 – 73NAD(P)UniRule annotation1 Publication3
    Nucleotide bindingi95 – 98NAD(P)UniRule annotation1 Publication4

    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)DescriptionActionsGraphical viewLength
    ChainiPRO_00001415021 – 2164-hydroxy-tetrahydrodipicolinate reductaseAdd BLAST216

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    STRINGi243274.TM1520.

    Structurei

    Secondary structure

    1216
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi2 – 6Combined sources5
    Turni7 – 9Combined sources3
    Helixi11 – 22Combined sources12
    Beta strandi26 – 32Combined sources7
    Beta strandi35 – 38Combined sources4
    Beta strandi43 – 47Combined sources5
    Helixi51 – 53Combined sources3
    Helixi54 – 64Combined sources11
    Beta strandi67 – 70Combined sources4
    Helixi77 – 86Combined sources10
    Turni87 – 89Combined sources3
    Beta strandi90 – 94Combined sources5
    Helixi100 – 115Combined sources16
    Turni116 – 118Combined sources3
    Beta strandi119 – 127Combined sources9
    Helixi137 – 145Combined sources9
    Beta strandi152 – 156Combined sources5
    Beta strandi163 – 169Combined sources7
    Beta strandi171 – 181Combined sources11
    Helixi185 – 198Combined sources14
    Beta strandi203 – 206Combined sources4
    Helixi208 – 212Combined sources5

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiQ9X1K8.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni137 – 138Substrate bindingUniRule annotation2

    Sequence similaritiesi

    Belongs to the DapB family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105DUK. Bacteria.
    COG0289. LUCA.
    InParanoidiQ9X1K8.
    KOiK00215.
    OMAiVICTTGY.

    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.
    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1VM6X-ray2.27A/B/C/D1-216[»]
    ProteinModelPortaliQ9X1K8.
    SMRiQ9X1K8.
    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.
    OMAiVICTTGY.

    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. 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.
    PROSITEiPS01298. DAPB. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    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: November 2, 2016
    This is version 125 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.