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Protein

4-hydroxy-tetrahydrodipicolinate synthase

Gene

dapA

Organism
Neisseria meningitidis serogroup B (strain MC58)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA).1 Publication

Catalytic activityi

Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H2O.UniRule annotation

Enzyme regulationi

Is allosterically feedback inhibited by lysine; the N.meningitidis enzyme is significantly more sensitive to lysine than the E.coli enzyme. Shows substrate inhibition by (S)-ASA, with a Ki of 1.7 mM.1 Publication

Kineticsi

kcat is 46.7 sec(-1).

  1. KM=0.50 mM for pyruvate1 Publication
  2. KM=0.052 mM for L-aspartate-4-semialdehyde1 Publication

    Pathwayi: L-lysine biosynthesis via DAP pathway

    This protein is involved in step 3 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 (lysC)
    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
    Sitei44Part of a proton relay during catalysisUniRule annotation1
    Binding sitei45PyruvateUniRule annotation1
    Sitei107Part of a proton relay during catalysisUniRule annotation1
    Active sitei133Proton donor/acceptorUniRule annotation1
    Active sitei161Schiff-base intermediate with substrateUniRule annotation1
    Binding sitei203Pyruvate; via carbonyl oxygenUniRule annotation1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Amino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis

    Keywords - Ligandi

    Schiff base

    Enzyme and pathway databases

    BRENDAi4.3.3.7. 3593.
    UniPathwayiUPA00034; UER00017.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    4-hydroxy-tetrahydrodipicolinate synthaseUniRule annotation (EC:4.3.3.7UniRule annotation)
    Short name:
    HTPA synthaseUniRule annotation
    Gene namesi
    Name:dapAUniRule annotation
    Ordered Locus Names:NMB0929
    OrganismiNeisseria meningitidis serogroup B (strain MC58)
    Taxonomic identifieri122586 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaNeisserialesNeisseriaceaeNeisseria
    Proteomesi
    • UP000000425 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_00001031311 – 2914-hydroxy-tetrahydrodipicolinate synthaseAdd BLAST291

    Proteomic databases

    PaxDbiQ9JZR4.

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    STRINGi122586.NMB0929.

    Structurei

    Secondary structure

    1291
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi4 – 8Combined sources5
    Helixi21 – 33Combined sources13
    Beta strandi38 – 43Combined sources6
    Turni44 – 47Combined sources4
    Helixi48 – 50Combined sources3
    Helixi53 – 67Combined sources15
    Beta strandi73 – 76Combined sources4
    Helixi82 – 94Combined sources13
    Beta strandi98 – 103Combined sources6
    Helixi112 – 125Combined sources14
    Beta strandi130 – 134Combined sources5
    Helixi136 – 139Combined sources4
    Helixi145 – 151Combined sources7
    Beta strandi157 – 162Combined sources6
    Helixi167 – 176Combined sources10
    Beta strandi182 – 185Combined sources4
    Helixi188 – 190Combined sources3
    Helixi191 – 196Combined sources6
    Beta strandi201 – 205Combined sources5
    Helixi206 – 208Combined sources3
    Helixi211 – 223Combined sources13
    Helixi226 – 240Combined sources15
    Turni241 – 244Combined sources4
    Beta strandi245 – 247Combined sources3
    Helixi250 – 258Combined sources9
    Helixi275 – 287Combined sources13

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3FLUX-ray2.00A/B/C/D1-291[»]
    ProteinModelPortaliQ9JZR4.
    SMRiQ9JZR4.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9JZR4.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the DapA family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105CDP. Bacteria.
    COG0329. LUCA.
    HOGENOMiHOG000173604.
    KOiK01714.
    OMAiGMDACVP.
    OrthoDBiPOG091H00C1.

    Family and domain databases

    CDDicd00950. DHDPS. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00418. DapA. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR005263. DapA.
    IPR002220. DapA-like.
    IPR020625. Schiff_base-form_aldolases_AS.
    IPR020624. Schiff_base-form_aldolases_CS.
    [Graphical view]
    PANTHERiPTHR12128. PTHR12128. 1 hit.
    PfamiPF00701. DHDPS. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001365. DHDPS. 1 hit.
    PRINTSiPR00146. DHPICSNTHASE.
    SMARTiSM01130. DHDPS. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00674. dapA. 1 hit.
    PROSITEiPS00665. DHDPS_1. 1 hit.
    PS00666. DHDPS_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9JZR4-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MLQGSLVALI TPMNQDGSIH YEQLRDLIDW HIENGTDGIV AVGTTGESAT
    60 70 80 90 100
    LSVEEHTAVI EAVVKHVAKR VPVIAGTGAN NTVEAIALSQ AAEKAGADYT
    110 120 130 140 150
    LSVVPYYNKP SQEGIYQHFK TIAEATSIPM IIYNVPGRTV VSMTNDTILR
    160 170 180 190 200
    LAEIPNIVGV KEASGNIGSN IELINRAPEG FVVLSGDDHT ALPFMLCGGH
    210 220 230 240 250
    GVITVAANAA PKLFADMCRA ALQGDIALAR ELNDRLIPIY DTMFCEPSPA
    260 270 280 290
    APKWAVSALG RCEPHVRLPL VPLTENGQAK VRAALKASGQ L
    Length:291
    Mass (Da):30,880
    Last modified:October 1, 2000 - v1
    Checksum:iAD5AF175BF32D842
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE002098 Genomic DNA. Translation: AAF41336.1.
    PIRiD81141.
    RefSeqiNP_273968.1. NC_003112.2.
    WP_002225337.1. NC_003112.2.

    Genome annotation databases

    EnsemblBacteriaiAAF41336; AAF41336; NMB0929.
    GeneIDi903050.
    KEGGinme:NMB0929.
    PATRICi20357327. VBINeiMen85645_1178.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AE002098 Genomic DNA. Translation: AAF41336.1.
    PIRiD81141.
    RefSeqiNP_273968.1. NC_003112.2.
    WP_002225337.1. NC_003112.2.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3FLUX-ray2.00A/B/C/D1-291[»]
    ProteinModelPortaliQ9JZR4.
    SMRiQ9JZR4.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi122586.NMB0929.

    Proteomic databases

    PaxDbiQ9JZR4.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAF41336; AAF41336; NMB0929.
    GeneIDi903050.
    KEGGinme:NMB0929.
    PATRICi20357327. VBINeiMen85645_1178.

    Phylogenomic databases

    eggNOGiENOG4105CDP. Bacteria.
    COG0329. LUCA.
    HOGENOMiHOG000173604.
    KOiK01714.
    OMAiGMDACVP.
    OrthoDBiPOG091H00C1.

    Enzyme and pathway databases

    UniPathwayiUPA00034; UER00017.
    BRENDAi4.3.3.7. 3593.

    Miscellaneous databases

    EvolutionaryTraceiQ9JZR4.

    Family and domain databases

    CDDicd00950. DHDPS. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00418. DapA. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR005263. DapA.
    IPR002220. DapA-like.
    IPR020625. Schiff_base-form_aldolases_AS.
    IPR020624. Schiff_base-form_aldolases_CS.
    [Graphical view]
    PANTHERiPTHR12128. PTHR12128. 1 hit.
    PfamiPF00701. DHDPS. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001365. DHDPS. 1 hit.
    PRINTSiPR00146. DHPICSNTHASE.
    SMARTiSM01130. DHDPS. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00674. dapA. 1 hit.
    PROSITEiPS00665. DHDPS_1. 1 hit.
    PS00666. DHDPS_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDAPA_NEIMB
    AccessioniPrimary (citable) accession number: Q9JZR4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 20, 2001
    Last sequence update: October 1, 2000
    Last modified: November 2, 2016
    This is version 104 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 synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB.Curated

    Keywords - Technical termi

    3D-structure, Allosteric enzyme, 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.