DCDA2_ARATH
ID DCDA2_ARATH Reviewed; 489 AA.
AC Q94A94; Q9LYI5; Q9SCX0;
DT 23-OCT-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Diaminopimelate decarboxylase 2, chloroplastic;
DE Short=DAP decarboxylase 2;
DE Short=DAPDC 2;
DE EC=4.1.1.20;
DE Flags: Precursor;
GN Name=LYSA2; Synonyms=diDi 18A-1f; OrderedLocusNames=At5g11880;
GN ORFNames=F14F18.50;
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=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(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 [MRNA] OF 345-489.
RC STRAIN=cv. Columbia; TISSUE=Root;
RX PubMed=11277426; DOI=10.1094/mpmi.2001.14.3.288;
RA Vercauteren I., van der Schueren E., Van Montagu M., Gheysen G.;
RT "Arabidopsis thaliana genes expressed in the early compatible interaction
RT with root-knot nematodes.";
RL Mol. Plant Microbe Interact. 14:288-299(2001).
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-51, CLEAVAGE OF TRANSIT PEPTIDE
RP [LARGE SCALE ANALYSIS] AFTER ALA-50, 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=CAB87661.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL163812; CAB87661.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED91734.1; -; Genomic_DNA.
DR EMBL; AY049266; AAK83608.1; -; mRNA.
DR EMBL; AY142042; AAM98306.1; -; mRNA.
DR EMBL; AJ249960; CAB62550.1; -; mRNA.
DR PIR; T48547; T48547.
DR RefSeq; NP_568252.1; NM_121226.5.
DR PDB; 6N2F; X-ray; 2.27 A; A/B=68-489.
DR PDBsum; 6N2F; -.
DR AlphaFoldDB; Q94A94; -.
DR SMR; Q94A94; -.
DR BioGRID; 16339; 6.
DR STRING; 3702.AT5G11880.1; -.
DR iPTMnet; Q94A94; -.
DR PaxDb; Q94A94; -.
DR PRIDE; Q94A94; -.
DR ProteomicsDB; 224560; -.
DR EnsemblPlants; AT5G11880.1; AT5G11880.1; AT5G11880.
DR GeneID; 831061; -.
DR Gramene; AT5G11880.1; AT5G11880.1; AT5G11880.
DR KEGG; ath:AT5G11880; -.
DR Araport; AT5G11880; -.
DR TAIR; locus:2143054; AT5G11880.
DR eggNOG; KOG0622; Eukaryota.
DR HOGENOM; CLU_026444_0_0_1; -.
DR InParanoid; Q94A94; -.
DR OMA; YCRSMAS; -.
DR OrthoDB; 725914at2759; -.
DR PhylomeDB; Q94A94; -.
DR BioCyc; ARA:AT5G11880-MON; -.
DR BioCyc; MetaCyc:AT5G11880-MON; -.
DR BRENDA; 4.1.1.20; 399.
DR UniPathway; UPA00034; UER00027.
DR PRO; PR:Q94A94; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q94A94; baseline and differential.
DR Genevisible; Q94A94; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005886; C:plasma membrane; 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..50
FT /note="Chloroplast"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 51..489
FT /note="Diaminopimelate decarboxylase 2, chloroplastic"
FT /id="PRO_0000307177"
FT ACT_SITE 416
FT /note="Proton donor"
FT /evidence="ECO:0000255"
FT BINDING 309
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 345..348
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 348
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 384
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 388
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 417
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 445
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250"
FT BINDING 445
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT MOD_RES 51
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT MOD_RES 130
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000250"
FT CONFLICT 346
FT /note="P -> L (in Ref. 4; CAB62550)"
FT /evidence="ECO:0000305"
FT STRAND 71..74
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 80..82
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 87..93
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 99..103
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 104..117
FT /evidence="ECO:0007829|PDB:6N2F"
FT TURN 118..120
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 123..128
FT /evidence="ECO:0007829|PDB:6N2F"
FT TURN 129..131
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 135..143
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 147..152
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 153..161
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 166..168
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 169..171
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 178..187
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 190..193
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 196..209
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 213..218
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 229..231
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 247..255
FT /evidence="ECO:0007829|PDB:6N2F"
FT TURN 258..260
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 261..274
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 277..296
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 303..310
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 324..329
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 332..338
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 341..345
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 347..351
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 352..354
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 355..367
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 370..376
FT /evidence="ECO:0007829|PDB:6N2F"
FT TURN 379..381
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 384..388
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 394..398
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 406..412
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 414..417
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 421..429
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 436..440
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 443..446
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 447..449
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 453..455
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 461..464
FT /evidence="ECO:0007829|PDB:6N2F"
FT STRAND 470..474
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 479..483
FT /evidence="ECO:0007829|PDB:6N2F"
FT HELIX 484..486
FT /evidence="ECO:0007829|PDB:6N2F"
SQ SEQUENCE 489 AA; 54164 MW; 5932A0ED08A8E17F CRC64;
MAAVTQFLSQ PSSIRGTLNQ YQLNQTSLSR IPFLSLKSTL KPLKRLSVKA AVSQNSTKTL
TKESASSFDH CFKKSSDGFL YCEGTKVQDI METVEKRPFY LYSKPQITRN LEAYKEALEG
VRSVIGYAIK ANNNLKILEH LRSLGCGAVL VSGNELRLAL LAGFDPTKCI FNGNGKSLED
LVLAAQEGVF VNVDSEFDLN NIVEASRISG KQVNVLLRIN PDVDPQVHPY VATGNKNSKF
GIRNEKLQWF LDEVKAHPKE LKLVGAHCHL GSTITKVDIF RDAAVLMIEY IDEIRRQGFE
VSYLNIGGGL GIDYYHAGAV LPTPMDLINT VRELVLSRDL NLIIEPGRSL IANTCCFVNH
VTGVKTNGTK NFIVIDGSMA ELIRPSLYDA YQHIELVSPT PPEAEVTKFD VVGPVCESAD
FLGKDRELPT PPQGAGLVVH DAGAYCMSMA STYNLKMRPP EYWVEEDGSI TKIRHAETFD
DHLRFFEGL
