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Q9LFG2

- DAPF_ARATH

UniProt

Q9LFG2 - DAPF_ARATH

Protein

Diaminopimelate epimerase, chloroplastic

Gene

DAPF

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 83 (01 Oct 2014)
      Sequence version 1 (01 Oct 2000)
      Previous versions | rss
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    Functioni

    Racemase that operates by a 'two-base' mechanism, which involves one active-site cysteine acting as a base to abstract the alpha-proton of an amino acid, while a second cysteine thiol functions as an acid to reprotonate the resulting planar carbanionic intermediate from the opposite face.1 Publication

    Catalytic activityi

    LL-2,6-diaminoheptanedioate = meso-diaminoheptanedioate.

    Enzyme regulationi

    Inhibited by aziridino-diaminopimelate (AziDAP).

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei88 – 881Substrate
    Binding sitei141 – 1411Substrate
    Active sitei150 – 1501
    Binding sitei239 – 2391Substrate
    Binding sitei278 – 2781Substrate
    Active sitei305 – 3051

    GO - Molecular functioni

    1. diaminopimelate epimerase activity Source: TAIR

    GO - Biological processi

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

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Amino-acid biosynthesis, Lysine biosynthesis

    Enzyme and pathway databases

    BioCyciARA:AT3G53580-MONOMER.
    UniPathwayiUPA00034; UER00025.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Diaminopimelate epimerase, chloroplastic (EC:5.1.1.7)
    Short name:
    DAP epimerase
    Gene namesi
    Name:DAPF
    Ordered Locus Names:At3g53580
    ORF Names:F4P12.280
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 3

    Organism-specific databases

    TAIRiAT3G53580.

    Subcellular locationi

    Plastidchloroplast Curated

    GO - Cellular componenti

    1. chloroplast Source: TAIR
    2. chloroplast stroma Source: TAIR

    Keywords - Cellular componenti

    Chloroplast, Plastid

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 5151ChloroplastSequence AnalysisAdd
    BLAST
    Chaini52 – 362311Diaminopimelate epimerase, chloroplasticPRO_0000307179Add
    BLAST

    Proteomic databases

    PaxDbiQ9LFG2.
    PRIDEiQ9LFG2.

    Expressioni

    Gene expression databases

    GenevestigatoriQ9LFG2.

    Interactioni

    Protein-protein interaction databases

    BioGridi9843. 1 interaction.
    STRINGi3702.AT3G53580.1-P.

    Structurei

    Secondary structure

    1
    362
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi77 – 859
    Beta strandi88 – 947
    Helixi105 – 1117
    Turni114 – 1163
    Beta strandi121 – 1288
    Beta strandi134 – 1418
    Helixi151 – 16414
    Beta strandi175 – 1773
    Beta strandi180 – 1867
    Beta strandi192 – 1954
    Helixi203 – 2053
    Beta strandi220 – 2256
    Beta strandi228 – 24720
    Helixi255 – 2573
    Helixi260 – 2689
    Beta strandi278 – 2869
    Beta strandi289 – 2968
    Turni297 – 2993
    Helixi306 – 31813
    Beta strandi324 – 3307
    Beta strandi333 – 3397
    Turni341 – 3433
    Beta strandi346 – 3505
    Beta strandi353 – 3619

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3EJXX-ray1.95A/B/C/D/E/F52-362[»]
    3EKMX-ray2.30A/B/C/D/E/F52-362[»]
    ProteinModelPortaliQ9LFG2.
    SMRiQ9LFG2. Positions 62-362.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9LFG2.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni151 – 1522Substrate binding
    Regioni296 – 2972Substrate binding
    Regioni306 – 3072Substrate binding

    Sequence similaritiesi

    Belongs to the diaminopimelate epimerase family.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiCOG0253.
    HOGENOMiHOG000220466.
    InParanoidiQ9LFG2.
    KOiK01778.
    OMAiLIVEPPY.
    PhylomeDBiQ9LFG2.

    Family and domain databases

    HAMAPiMF_00197. DAP_epimerase.
    InterProiIPR018510. DAP_epimerase_AS.
    IPR001653. DAP_epimerase_DapF.
    [Graphical view]
    PANTHERiPTHR31689. PTHR31689. 1 hit.
    PfamiPF01678. DAP_epimerase. 2 hits.
    [Graphical view]
    TIGRFAMsiTIGR00652. DapF. 1 hit.
    PROSITEiPS01326. DAP_EPIMERASE. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

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

    Q9LFG2-1 [UniParc]FASTAAdd to Basket

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    MEIAAVSTVS VAPQSRRVSN AFSRNLGSVS SLSFGFFEKE YCFKSPSLRV    50
    SAAASMDAVT AEKFSPASFL DKKETGVLHF VKYHGLGNDF ILVDNRDSSE 100
    PKITQEQAAK LCDRNFGVGA DGVIFAMPGV NGTDYAMRIF NSDGSEPEMC 150
    GNGVRCFARF IAELENLQGK HSFTIHTGAG LIVPEIQDDG QVKVDMGTPI 200
    LKAQDVPTKL SGNKGEAVVE AELVVDGVSW NVTCVSMGNP HCITFGKKGG 250
    PNLKVDDLNL PEIGPKFEHH EMFPARTNTE FVEVLSRSHL KMRVWERGAG 300
    ATLACGTGAC ALVVAAVLEG RADRKCTVDL PGGPLEIEWK QEDNHIYMTG 350
    PAEAVFYGSA LL 362
    Length:362
    Mass (Da):38,984
    Last modified:October 1, 2000 - v1
    Checksum:iB2C18C4714BAA543
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AL132966 Genomic DNA. Translation: CAB67665.1.
    CP002686 Genomic DNA. Translation: AEE79113.1.
    AY126996 mRNA. Translation: AAM83223.1.
    AY143871 mRNA. Translation: AAN28810.1.
    PIRiT45898.
    RefSeqiNP_190926.1. NM_115218.3.
    UniGeneiAt.21032.

    Genome annotation databases

    EnsemblPlantsiAT3G53580.1; AT3G53580.1; AT3G53580.
    GeneIDi824526.
    KEGGiath:AT3G53580.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AL132966 Genomic DNA. Translation: CAB67665.1 .
    CP002686 Genomic DNA. Translation: AEE79113.1 .
    AY126996 mRNA. Translation: AAM83223.1 .
    AY143871 mRNA. Translation: AAN28810.1 .
    PIRi T45898.
    RefSeqi NP_190926.1. NM_115218.3.
    UniGenei At.21032.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3EJX X-ray 1.95 A/B/C/D/E/F 52-362 [» ]
    3EKM X-ray 2.30 A/B/C/D/E/F 52-362 [» ]
    ProteinModelPortali Q9LFG2.
    SMRi Q9LFG2. Positions 62-362.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 9843. 1 interaction.
    STRINGi 3702.AT3G53580.1-P.

    Proteomic databases

    PaxDbi Q9LFG2.
    PRIDEi Q9LFG2.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT3G53580.1 ; AT3G53580.1 ; AT3G53580 .
    GeneIDi 824526.
    KEGGi ath:AT3G53580.

    Organism-specific databases

    TAIRi AT3G53580.

    Phylogenomic databases

    eggNOGi COG0253.
    HOGENOMi HOG000220466.
    InParanoidi Q9LFG2.
    KOi K01778.
    OMAi LIVEPPY.
    PhylomeDBi Q9LFG2.

    Enzyme and pathway databases

    UniPathwayi UPA00034 ; UER00025 .
    BioCyci ARA:AT3G53580-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q9LFG2.
    PROi Q9LFG2.

    Gene expression databases

    Genevestigatori Q9LFG2.

    Family and domain databases

    HAMAPi MF_00197. DAP_epimerase.
    InterProi IPR018510. DAP_epimerase_AS.
    IPR001653. DAP_epimerase_DapF.
    [Graphical view ]
    PANTHERi PTHR31689. PTHR31689. 1 hit.
    Pfami PF01678. DAP_epimerase. 2 hits.
    [Graphical view ]
    TIGRFAMsi TIGR00652. DapF. 1 hit.
    PROSITEi PS01326. DAP_EPIMERASE. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana."
      Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B., Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M., Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V., Choisne N., Artiguenave F.
      , Robert C., Brottier P., Wincker P., Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H., Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H., Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A., Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H., Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J., Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B., Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D., de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E., Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G., Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X., Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M., Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B., Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J., Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C., Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y., Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K., Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
      Nature 408:820-822(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    2. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    3. "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.
    4. "Biosynthesis of lysine in plants: evidence for a variant of the known bacterial pathways."
      Hudson A.O., Bless C., Macedo P., Chatterjee S.P., Singh B.K., Gilvarg C., Leustek T.
      Biochim. Biophys. Acta 1721:27-36(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    5. "Crystal structure of diaminopimelate epimerase from Arabidopsis thaliana, an amino acid racemase critical for L-lysine biosynthesis."
      Pillai B., Moorthie V.A., van Belkum M.J., Marcus S.L., Cherney M.M., Diaper C.M., Vederas J.C., James M.N.
      J. Mol. Biol. 385:580-594(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 52-362 IN COMPLEX WITH INHIBITORS.

    Entry informationi

    Entry nameiDAPF_ARATH
    AccessioniPrimary (citable) accession number: Q9LFG2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 23, 2007
    Last sequence update: October 1, 2000
    Last modified: October 1, 2014
    This is version 83 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    This enzyme requires no cofactors.

    Keywords - Technical termi

    3D-structure, 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