DCDA1_ARATH
ID DCDA1_ARATH Reviewed; 484 AA.
AC Q949X7; Q9LUL0;
DT 23-OCT-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 137.
DE RecName: Full=Diaminopimelate decarboxylase 1, chloroplastic;
DE Short=DAP decarboxylase 1;
DE Short=DAPDC 1;
DE EC=4.1.1.20;
DE Flags: Precursor;
GN Name=LYSA1; OrderedLocusNames=At3g14390; ORFNames=MLN21.17;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION.
RX PubMed=15652176; DOI=10.1016/j.bbagen.2004.09.008;
RA Hudson A.O., Bless C., Macedo P., Chatterjee S.P., Singh B.K., Gilvarg C.,
RA Leustek T.;
RT "Biosynthesis of lysine in plants: evidence for a variant of the known
RT bacterial pathways.";
RL Biochim. Biophys. Acta 1721:27-36(2005).
RN [6]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-50, CLEAVAGE OF TRANSIT PEPTIDE
RP [LARGE SCALE ANALYSIS] AFTER ALA-49, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
CC -!- FUNCTION: Specifically catalyzes the decarboxylation of meso-
CC diaminopimelate (meso-DAP) to L-lysine. {ECO:0000269|PubMed:15652176}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + meso-2,6-diaminoheptanedioate = CO2 + L-lysine;
CC Xref=Rhea:RHEA:15101, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:32551, ChEBI:CHEBI:57791; EC=4.1.1.20;
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000250};
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC pathway; L-lysine from DL-2,6-diaminopimelate: step 1/1.
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-II family.
CC LysA subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB01044.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AB022220; BAB01044.1; ALT_INIT; Genomic_DNA.
DR EMBL; CP002686; AEE75511.1; -; Genomic_DNA.
DR EMBL; AY050823; AAK92758.1; -; mRNA.
DR EMBL; AF227913; AAL55653.1; -; mRNA.
DR EMBL; AY122998; AAM67531.1; -; mRNA.
DR EMBL; AY088418; AAM65955.1; -; mRNA.
DR RefSeq; NP_188056.1; NM_112297.3.
DR PDB; 6N2A; X-ray; 1.88 A; A/B=63-484.
DR PDBsum; 6N2A; -.
DR AlphaFoldDB; Q949X7; -.
DR SMR; Q949X7; -.
DR BioGRID; 5994; 5.
DR IntAct; Q949X7; 1.
DR STRING; 3702.AT3G14390.1; -.
DR iPTMnet; Q949X7; -.
DR PaxDb; Q949X7; -.
DR PRIDE; Q949X7; -.
DR ProteomicsDB; 224170; -.
DR EnsemblPlants; AT3G14390.1; AT3G14390.1; AT3G14390.
DR GeneID; 820660; -.
DR Gramene; AT3G14390.1; AT3G14390.1; AT3G14390.
DR KEGG; ath:AT3G14390; -.
DR Araport; AT3G14390; -.
DR TAIR; locus:2091055; AT3G14390.
DR eggNOG; KOG0622; Eukaryota.
DR HOGENOM; CLU_026444_0_0_1; -.
DR InParanoid; Q949X7; -.
DR OMA; HGNAKSP; -.
DR OrthoDB; 725914at2759; -.
DR PhylomeDB; Q949X7; -.
DR BioCyc; ARA:AT3G14390-MON; -.
DR BioCyc; MetaCyc:AT3G14390-MON; -.
DR BRENDA; 4.1.1.20; 399.
DR UniPathway; UPA00034; UER00027.
DR PRO; PR:Q949X7; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q949X7; baseline and differential.
DR Genevisible; Q949X7; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; HDA:TAIR.
DR GO; GO:0008836; F:diaminopimelate decarboxylase activity; IBA:GO_Central.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IBA:GO_Central.
DR CDD; cd06828; PLPDE_III_DapDC; 1.
DR Gene3D; 2.40.37.10; -; 1.
DR Gene3D; 3.20.20.10; -; 1.
DR HAMAP; MF_02120; LysA; 1.
DR InterPro; IPR009006; Ala_racemase/Decarboxylase_C.
DR InterPro; IPR002986; DAP_deCOOHase_LysA.
DR InterPro; IPR022643; De-COase2_C.
DR InterPro; IPR022657; De-COase2_CS.
DR InterPro; IPR022644; De-COase2_N.
DR InterPro; IPR022653; De-COase2_pyr-phos_BS.
DR InterPro; IPR000183; Orn/DAP/Arg_de-COase.
DR InterPro; IPR029066; PLP-binding_barrel.
DR Pfam; PF02784; Orn_Arg_deC_N; 1.
DR Pfam; PF00278; Orn_DAP_Arg_deC; 1.
DR PRINTS; PR01181; DAPDCRBXLASE.
DR PRINTS; PR01179; ODADCRBXLASE.
DR SUPFAM; SSF50621; SSF50621; 1.
DR SUPFAM; SSF51419; SSF51419; 1.
DR TIGRFAMs; TIGR01048; lysA; 1.
DR PROSITE; PS00878; ODR_DC_2_1; 1.
DR PROSITE; PS00879; ODR_DC_2_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Amino-acid biosynthesis; Chloroplast;
KW Decarboxylase; Lyase; Lysine biosynthesis; Plastid; Pyridoxal phosphate;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..49
FT /note="Chloroplast"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 50..484
FT /note="Diaminopimelate decarboxylase 1, chloroplastic"
FT /id="PRO_0000307176"
FT REGION 1..30
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 411
FT /note="Proton donor"
FT /evidence="ECO:0000255"
FT BINDING 304
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 340..343
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 343
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 379
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 383
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 412
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 440
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 440
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT MOD_RES 50
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT MOD_RES 125
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
FT STRAND 66..69
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 75..77
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 82..88
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 94..98
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 99..112
FT /evidence="ECO:0007829|PDB:6N2A"
FT TURN 113..115
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 118..123
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 124..126
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 130..138
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 142..147
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 148..156
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 161..163
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 164..166
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 173..182
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 185..188
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 191..204
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 208..215
FT /evidence="ECO:0007829|PDB:6N2A"
FT TURN 220..222
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 224..232
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 234..238
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 239..241
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 242..251
FT /evidence="ECO:0007829|PDB:6N2A"
FT TURN 253..255
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 256..262
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 267..269
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 273..291
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 298..300
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 319..324
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 327..333
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 336..339
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 343..346
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 347..349
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 350..361
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 366..371
FT /evidence="ECO:0007829|PDB:6N2A"
FT TURN 374..376
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 379..383
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 389..393
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 401..407
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 409..412
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 416..424
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 431..436
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 438..441
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 442..444
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 448..450
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 456..459
FT /evidence="ECO:0007829|PDB:6N2A"
FT STRAND 465..469
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 474..478
FT /evidence="ECO:0007829|PDB:6N2A"
FT HELIX 479..481
FT /evidence="ECO:0007829|PDB:6N2A"
SQ SEQUENCE 484 AA; 53557 MW; 9CD379610A8676D9 CRC64;
MAAATQFLSQ PSSLNPHQLK NQTSQRSRSI PVLSLKSTLK PLKRLSVKAA VVSQNSSKTV
TKFDHCFKKS SDGFLYCEGT KVEDIMESVE RRPFYLYSKP QITRNLEAYK EALEGVSSVI
GYAIKANNNL KILEHLRSLG CGAVLVSGNE LRLALRAGFD PTKCIFNGNG KSLEDLVLAA
QEGVFVNVDS EFDLNNIVEA SRISGKQVNV LLRINPDVDP QVHPYVATGN KNSKFGIRNE
KLQWFLDQVK AHPKELKLVG AHCHLGSTIT KVDIFRDAAV LMIEYIDEIR RQGFEVSYLN
IGGGLGIDYY HAGAVLPTPM DLINTVRELV LSRDLNLIIE PGRSLIANTC CFVNHVTGVK
TNGTKNFIVI DGSMAELIRP SLYDAYQHIE LVSPPPAEAE VTKFDVVGPV CESADFLGKD
RELPTPPQGA GLVVHDAGAY CMSMASTYNL KMRPPEYWVE EDGSITKIRH AETFDDHLRF
FEGL
