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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. no protein annotated in this organism
    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)LengthDescriptionGraphical viewFeature identifierActions
    Sitei44 – 441Part of a proton relay during catalysisUniRule annotation
    Binding sitei45 – 451PyruvateUniRule annotation
    Sitei107 – 1071Part of a proton relay during catalysisUniRule annotation
    Active sitei133 – 1331Proton donor/acceptorUniRule annotation
    Active sitei161 – 1611Schiff-base intermediate with substrateUniRule annotation
    Binding sitei203 – 2031Pyruvate; via carbonyl oxygenUniRule annotation

    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

    BioCyciNMEN122586:GHGG-967-MONOMER.
    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)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 2912914-hydroxy-tetrahydrodipicolinate synthasePRO_0000103131Add
    BLAST

    Proteomic databases

    PaxDbiQ9JZR4.

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    STRINGi122586.NMB0929.

    Structurei

    Secondary structure

    1
    291
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi4 – 85Combined sources
    Helixi21 – 3313Combined sources
    Beta strandi38 – 436Combined sources
    Turni44 – 474Combined sources
    Helixi48 – 503Combined sources
    Helixi53 – 6715Combined sources
    Beta strandi73 – 764Combined sources
    Helixi82 – 9413Combined sources
    Beta strandi98 – 1036Combined sources
    Helixi112 – 12514Combined sources
    Beta strandi130 – 1345Combined sources
    Helixi136 – 1394Combined sources
    Helixi145 – 1517Combined sources
    Beta strandi157 – 1626Combined sources
    Helixi167 – 17610Combined sources
    Beta strandi182 – 1854Combined sources
    Helixi188 – 1903Combined sources
    Helixi191 – 1966Combined sources
    Beta strandi201 – 2055Combined sources
    Helixi206 – 2083Combined sources
    Helixi211 – 22313Combined sources
    Helixi226 – 24015Combined sources
    Turni241 – 2444Combined sources
    Beta strandi245 – 2473Combined sources
    Helixi250 – 2589Combined sources
    Helixi275 – 28713Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3FLUX-ray2.00A/B/C/D1-291[»]
    ProteinModelPortaliQ9JZR4.
    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.
    OrthoDBiEOG6W7235.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00418. DapA.
    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
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3FLUX-ray2.00A/B/C/D1-291[»]
    ProteinModelPortaliQ9JZR4.
    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.
    OrthoDBiEOG6W7235.

    Enzyme and pathway databases

    UniPathwayiUPA00034; UER00017.
    BioCyciNMEN122586:GHGG-967-MONOMER.
    BRENDAi4.3.3.7. 3593.

    Miscellaneous databases

    EvolutionaryTraceiQ9JZR4.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00418. DapA.
    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...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: MC58.
    2. "Cloning and characterisation of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis."
      Devenish S.R., Huisman F.H., Parker E.J., Hadfield A.T., Gerrard J.A.
      Biochim. Biophys. Acta 1794:1168-1174(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), FUNCTION, KINETIC PARAMETERS, ENZYME REGULATION, IDENTIFICATION BY MASS SPECTROMETRY, SUBUNIT.
      Strain: MC58.

    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: May 11, 2016
    This is version 102 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.