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Q9FVC8

- DAPA2_ARATH

UniProt

Q9FVC8 - DAPA2_ARATH

Protein

4-hydroxy-tetrahydrodipicolinate synthase 2, chloroplastic

Gene

DHDPS2

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 104 (01 Oct 2014)
      Sequence version 2 (20 Jun 2001)
      Previous versions | rss
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    • Comment

    Functioni

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

    Catalytic activityi

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

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei107 – 1071Part of a proton relay during catalysisBy similarity
    Binding sitei108 – 1081PyruvateBy similarity
    Sitei170 – 1701Part of a proton relay during catalysisBy similarity
    Active sitei194 – 1941Proton donor/acceptorBy similarity
    Active sitei222 – 2221Schiff-base intermediate with substrateBy similarity
    Binding sitei261 – 2611Pyruvate; via carbonyl oxygenBy similarity

    GO - Molecular functioni

    1. 4-hydroxy-tetrahydrodipicolinate synthase Source: TAIR

    GO - Biological processi

    1. diaminopimelate biosynthetic process Source: UniProtKB-KW
    2. lysine biosynthetic process via diaminopimelate Source: UniProtKB-UniPathway

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Amino-acid biosynthesis, Diaminopimelate biosynthesis, Lysine biosynthesis

    Keywords - Ligandi

    Schiff base

    Enzyme and pathway databases

    BioCyciARA:AT2G45440-MONOMER.
    UniPathwayiUPA00034; UER00017.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    4-hydroxy-tetrahydrodipicolinate synthase 2, chloroplastic (EC:4.3.3.7)
    Short name:
    HTPA synthase 2
    Gene namesi
    Name:DHDPS2
    Ordered Locus Names:At2g45440
    ORF Names:F4L23.5
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 2

    Organism-specific databases

    TAIRiAT2G45440.

    Subcellular locationi

    GO - Cellular componenti

    1. chloroplast Source: TAIR

    Keywords - Cellular componenti

    Chloroplast, Plastid

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 3939ChloroplastSequence AnalysisAdd
    BLAST
    Chaini40 – 3653264-hydroxy-tetrahydrodipicolinate synthase 2, chloroplasticPRO_0000007198Add
    BLAST

    Proteomic databases

    PaxDbiQ9FVC8.
    PRIDEiQ9FVC8.

    Expressioni

    Gene expression databases

    ArrayExpressiQ9FVC8.
    GenevestigatoriQ9FVC8.

    Interactioni

    Protein-protein interaction databases

    BioGridi4488. 2 interactions.
    STRINGi3702.AT2G45440.1-P.

    Structurei

    Secondary structure

    1
    365
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi60 – 645
    Beta strandi68 – 714
    Beta strandi80 – 823
    Helixi84 – 9613
    Beta strandi101 – 1066
    Turni107 – 1104
    Helixi111 – 1133
    Helixi116 – 13015
    Turni131 – 1333
    Beta strandi134 – 1396
    Helixi145 – 15713
    Beta strandi161 – 1666
    Helixi175 – 1839
    Helixi186 – 1883
    Beta strandi191 – 1955
    Helixi197 – 2004
    Helixi206 – 2127
    Beta strandi218 – 2236
    Helixi227 – 2359
    Beta strandi240 – 2423
    Helixi245 – 2473
    Helixi248 – 2547
    Beta strandi259 – 2635
    Helixi264 – 2663
    Helixi269 – 2779
    Helixi282 – 29514
    Beta strandi297 – 2993
    Helixi302 – 3109
    Beta strandi316 – 3194
    Helixi327 – 34014
    Helixi342 – 3443
    Beta strandi345 – 3495
    Helixi356 – 3583
    Beta strandi360 – 3634

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4DPPX-ray2.00A/B39-365[»]
    4DPQX-ray2.20A/B39-365[»]
    ProteinModelPortaliQ9FVC8.
    SMRiQ9FVC8. Positions 59-365.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the DapA family.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG0329.
    HOGENOMiHOG000173604.
    InParanoidiQ9FVC8.
    KOiK01714.
    OMAiMLYSGDD.
    PhylomeDBiQ9FVC8.

    Family and domain databases

    Gene3Di3.20.20.70. 1 hit.
    HAMAPiMF_00418. DapA.
    InterProiIPR013785. Aldolase_TIM.
    IPR005263. DapA.
    IPR002220. DapA-like.
    IPR020625. Dihydrodipicolinate_synth_AS.
    IPR020624. Dihydrodipicolinate_synth_CS.
    [Graphical view]
    PANTHERiPTHR12128. PTHR12128. 1 hit.
    PfamiPF00701. DHDPS. 1 hit.
    [Graphical view]
    PRINTSiPR00146. DHPICSNTHASE.
    TIGRFAMsiTIGR00674. dapA. 1 hit.
    PROSITEiPS00665. DHDPS_1. 1 hit.
    PS00666. DHDPS_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q9FVC8-1 [UniParc]FASTAAdd to Basket

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    MAALKGYGLC SMDSALQFPC PKLFNSYKRR SSKWVSPKAA VVPNFHLPMR    50
    SLEVKNRTNT DDIKALRVIT AIKTPYLPDG RFDLEAYDDL VNIQIQNGAE 100
    GVIVGGTTGE GQLMSWDEHI MLIGHTVNCF GGSIKVIGNT GSNSTREAIH 150
    ATEQGFAVGM HAALHINPYY GKTSIEGLIA HFQSVLHMGP TIIYNVPGRT 200
    GQDIPPRAIF KLSQNPNLAG VKECVGNKRV EEYTENGVVV WSGNDDECHD 250
    SRWDYGATGV ISVTSNLVPG LMRKLMFEGR NSSLNSKLLP LMAWLFHEPN 300
    PIGINTALAQ LGVSRPVFRL PYVPLPLSKR LEFVKLVKEI GREHFVGEKD 350
    VQALDDDDFI LIGRY 365
    Length:365
    Mass (Da):40,292
    Last modified:June 20, 2001 - v2
    Checksum:i43BECEF1FC3E557A
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti26 – 261S → G in AAG28565. (PubMed:11069709)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF200325 Genomic DNA. Translation: AAG28565.1.
    AC002387 Genomic DNA. Translation: AAB82620.1.
    CP002685 Genomic DNA. Translation: AEC10554.1.
    BT004823 mRNA. Translation: AAO44089.1.
    PIRiE84890.
    RefSeqiNP_182068.1. NM_130106.2.
    UniGeneiAt.12311.

    Genome annotation databases

    EnsemblPlantsiAT2G45440.1; AT2G45440.1; AT2G45440.
    GeneIDi819152.
    KEGGiath:AT2G45440.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF200325 Genomic DNA. Translation: AAG28565.1 .
    AC002387 Genomic DNA. Translation: AAB82620.1 .
    CP002685 Genomic DNA. Translation: AEC10554.1 .
    BT004823 mRNA. Translation: AAO44089.1 .
    PIRi E84890.
    RefSeqi NP_182068.1. NM_130106.2.
    UniGenei At.12311.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4DPP X-ray 2.00 A/B 39-365 [» ]
    4DPQ X-ray 2.20 A/B 39-365 [» ]
    ProteinModelPortali Q9FVC8.
    SMRi Q9FVC8. Positions 59-365.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 4488. 2 interactions.
    STRINGi 3702.AT2G45440.1-P.

    Proteomic databases

    PaxDbi Q9FVC8.
    PRIDEi Q9FVC8.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT2G45440.1 ; AT2G45440.1 ; AT2G45440 .
    GeneIDi 819152.
    KEGGi ath:AT2G45440.

    Organism-specific databases

    TAIRi AT2G45440.

    Phylogenomic databases

    eggNOGi COG0329.
    HOGENOMi HOG000173604.
    InParanoidi Q9FVC8.
    KOi K01714.
    OMAi MLYSGDD.
    PhylomeDBi Q9FVC8.

    Enzyme and pathway databases

    UniPathwayi UPA00034 ; UER00017 .
    BioCyci ARA:AT2G45440-MONOMER.

    Gene expression databases

    ArrayExpressi Q9FVC8.
    Genevestigatori Q9FVC8.

    Family and domain databases

    Gene3Di 3.20.20.70. 1 hit.
    HAMAPi MF_00418. DapA.
    InterProi IPR013785. Aldolase_TIM.
    IPR005263. DapA.
    IPR002220. DapA-like.
    IPR020625. Dihydrodipicolinate_synth_AS.
    IPR020624. Dihydrodipicolinate_synth_CS.
    [Graphical view ]
    PANTHERi PTHR12128. PTHR12128. 1 hit.
    Pfami PF00701. DHDPS. 1 hit.
    [Graphical view ]
    PRINTSi PR00146. DHPICSNTHASE.
    TIGRFAMsi TIGR00674. dapA. 1 hit.
    PROSITEi PS00665. DHDPS_1. 1 hit.
    PS00666. DHDPS_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Identification of an Arabidopsis thaliana mutant accumulating threonine resulting from mutation in a new dihydrodipicolinate synthase gene."
      Sarrobert C., Thibaud M.-C., Contard-David P., Gineste S., Bechtold N., Robaglia C., Nussaume L.
      Plant J. 24:357-367(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: cv. Wassilewskija.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.

    Entry informationi

    Entry nameiDAPA2_ARATH
    AccessioniPrimary (citable) accession number: Q9FVC8
    Secondary accession number(s): O22129
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 20, 2001
    Last sequence update: June 20, 2001
    Last modified: October 1, 2014
    This is version 104 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant 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. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    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