ID   DAPF_ARATH              Reviewed;         362 AA.
AC   Q9LFG2;
DT   23-OCT-2007, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2000, sequence version 1.
DT   27-MAR-2024, entry version 128.
DE   RecName: Full=Diaminopimelate epimerase, chloroplastic;
DE            Short=DAP epimerase;
DE            EC=5.1.1.7;
DE   Flags: Precursor;
GN   Name=DAPF; OrderedLocusNames=At3g53580; ORFNames=F4P12.280;
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=11130713; DOI=10.1038/35048706;
RA   Salanoubat M., Lemcke K., Rieger M., Ansorge W., Unseld M., Fartmann B.,
RA   Valle G., Bloecker H., Perez-Alonso M., Obermaier B., Delseny M.,
RA   Boutry M., Grivell L.A., Mache R., Puigdomenech P., De Simone V.,
RA   Choisne N., Artiguenave F., Robert C., Brottier P., Wincker P.,
RA   Cattolico L., Weissenbach J., Saurin W., Quetier F., Schaefer M.,
RA   Mueller-Auer S., Gabel C., Fuchs M., Benes V., Wurmbach E., Drzonek H.,
RA   Erfle H., Jordan N., Bangert S., Wiedelmann R., Kranz H., Voss H.,
RA   Holland R., Brandt P., Nyakatura G., Vezzi A., D'Angelo M., Pallavicini A.,
RA   Toppo S., Simionati B., Conrad A., Hornischer K., Kauer G., Loehnert T.-H.,
RA   Nordsiek G., Reichelt J., Scharfe M., Schoen O., Bargues M., Terol J.,
RA   Climent J., Navarro P., Collado C., Perez-Perez A., Ottenwaelder B.,
RA   Duchemin D., Cooke R., Laudie M., Berger-Llauro C., Purnelle B., Masuy D.,
RA   de Haan M., Maarse A.C., Alcaraz J.-P., Cottet A., Casacuberta E.,
RA   Monfort A., Argiriou A., Flores M., Liguori R., Vitale D., Mannhaupt G.,
RA   Haase D., Schoof H., Rudd S., Zaccaria P., Mewes H.-W., Mayer K.F.X.,
RA   Kaul S., Town C.D., Koo H.L., Tallon L.J., Jenkins J., Rooney T., Rizzo M.,
RA   Walts A., Utterback T., Fujii C.Y., Shea T.P., Creasy T.H., Haas B.,
RA   Maiti R., Wu D., Peterson J., Van Aken S., Pai G., Militscher J.,
RA   Sellers P., Gill J.E., Feldblyum T.V., Preuss D., Lin X., Nierman W.C.,
RA   Salzberg S.L., White O., Venter J.C., Fraser C.M., Kaneko T., Nakamura Y.,
RA   Sato S., Kato T., Asamizu E., Sasamoto S., Kimura T., Idesawa K.,
RA   Kawashima K., Kishida Y., Kiyokawa C., Kohara M., Matsumoto M., Matsuno A.,
RA   Muraki A., Nakayama S., Nakazaki N., Shinpo S., Takeuchi C., Wada T.,
RA   Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT   "Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.";
RL   Nature 408:820-822(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   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   [5]
RP   ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-53, CLEAVAGE OF TRANSIT PEPTIDE
RP   [LARGE SCALE ANALYSIS] AFTER ALA-52, 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).
RN   [6]
RP   X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 52-362 IN COMPLEX WITH
RP   INHIBITORS.
RX   PubMed=19013471; DOI=10.1016/j.jmb.2008.10.072;
RA   Pillai B., Moorthie V.A., van Belkum M.J., Marcus S.L., Cherney M.M.,
RA   Diaper C.M., Vederas J.C., James M.N.;
RT   "Crystal structure of diaminopimelate epimerase from Arabidopsis thaliana,
RT   an amino acid racemase critical for L-lysine biosynthesis.";
RL   J. Mol. Biol. 385:580-594(2009).
CC   -!- FUNCTION: Racemase that operates by a 'two-base' mechanism, which
CC       involves one active-site cysteine acting as a base to abstract the
CC       alpha-proton of an amino acid, while a second cysteine thiol functions
CC       as an acid to reprotonate the resulting planar carbanionic intermediate
CC       from the opposite face. {ECO:0000269|PubMed:15652176}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=(2S,6S)-2,6-diaminoheptanedioate = meso-2,6-
CC         diaminoheptanedioate; Xref=Rhea:RHEA:15393, ChEBI:CHEBI:57609,
CC         ChEBI:CHEBI:57791; EC=5.1.1.7;
CC   -!- ACTIVITY REGULATION: Inhibited by aziridino-diaminopimelate (AziDAP).
CC   -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC       pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step 1/1.
CC   -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
CC   -!- MISCELLANEOUS: This enzyme requires no cofactors.
CC   -!- SIMILARITY: Belongs to the diaminopimelate epimerase family.
CC       {ECO:0000305}.
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DR   EMBL; AL132966; CAB67665.1; -; Genomic_DNA.
DR   EMBL; CP002686; AEE79113.1; -; Genomic_DNA.
DR   EMBL; AY126996; AAM83223.1; -; mRNA.
DR   EMBL; AY143871; AAN28810.1; -; mRNA.
DR   PIR; T45898; T45898.
DR   RefSeq; NP_190926.1; NM_115218.4.
DR   PDB; 3EJX; X-ray; 1.95 A; A/B/C/D/E/F=52-362.
DR   PDB; 3EKM; X-ray; 2.30 A; A/B/C/D/E/F=52-362.
DR   PDBsum; 3EJX; -.
DR   PDBsum; 3EKM; -.
DR   AlphaFoldDB; Q9LFG2; -.
DR   SMR; Q9LFG2; -.
DR   BioGRID; 9843; 26.
DR   IntAct; Q9LFG2; 1.
DR   STRING; 3702.Q9LFG2; -.
DR   iPTMnet; Q9LFG2; -.
DR   MetOSite; Q9LFG2; -.
DR   PaxDb; 3702-AT3G53580-1; -.
DR   ProteomicsDB; 224583; -.
DR   EnsemblPlants; AT3G53580.1; AT3G53580.1; AT3G53580.
DR   GeneID; 824526; -.
DR   Gramene; AT3G53580.1; AT3G53580.1; AT3G53580.
DR   KEGG; ath:AT3G53580; -.
DR   Araport; AT3G53580; -.
DR   TAIR; AT3G53580; -.
DR   eggNOG; ENOG502QQKJ; Eukaryota.
DR   HOGENOM; CLU_053306_2_1_1; -.
DR   InParanoid; Q9LFG2; -.
DR   OMA; CVGLFAY; -.
DR   OrthoDB; 472077at2759; -.
DR   PhylomeDB; Q9LFG2; -.
DR   BioCyc; ARA:AT3G53580-MONOMER; -.
DR   BRENDA; 5.1.1.7; 399.
DR   UniPathway; UPA00034; UER00025.
DR   EvolutionaryTrace; Q9LFG2; -.
DR   PRO; PR:Q9LFG2; -.
DR   Proteomes; UP000006548; Chromosome 3.
DR   ExpressionAtlas; Q9LFG2; baseline and differential.
DR   GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR   GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR   GO; GO:0008837; F:diaminopimelate epimerase activity; IEA:UniProtKB-EC.
DR   GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniPathway.
DR   HAMAP; MF_00197; DAP_epimerase; 1.
DR   InterPro; IPR018510; DAP_epimerase_AS.
DR   InterPro; IPR001653; DAP_epimerase_DapF.
DR   NCBIfam; TIGR00652; DapF; 1.
DR   PANTHER; PTHR31689:SF0; DIAMINOPIMELATE EPIMERASE; 1.
DR   PANTHER; PTHR31689; DIAMINOPIMELATE EPIMERASE, CHLOROPLASTIC; 1.
DR   Pfam; PF01678; DAP_epimerase; 2.
DR   SUPFAM; SSF54506; Diaminopimelate epimerase-like; 2.
DR   PROSITE; PS01326; DAP_EPIMERASE; 1.
DR   Genevisible; Q9LFG2; AT.
PE   1: Evidence at protein level;
KW   3D-structure; Acetylation; Amino-acid biosynthesis; Chloroplast; Isomerase;
KW   Lysine biosynthesis; Plastid; Reference proteome; Transit peptide.
FT   TRANSIT         1..52
FT                   /note="Chloroplast"
FT                   /evidence="ECO:0000255, ECO:0007744|PubMed:22223895"
FT   CHAIN           53..362
FT                   /note="Diaminopimelate epimerase, chloroplastic"
FT                   /id="PRO_0000307179"
FT   ACT_SITE        150
FT   ACT_SITE        305
FT   BINDING         88
FT                   /ligand="substrate"
FT   BINDING         141
FT                   /ligand="substrate"
FT   BINDING         151..152
FT                   /ligand="substrate"
FT   BINDING         239
FT                   /ligand="substrate"
FT   BINDING         278
FT                   /ligand="substrate"
FT   BINDING         296..297
FT                   /ligand="substrate"
FT   BINDING         306..307
FT                   /ligand="substrate"
FT   MOD_RES         53
FT                   /note="N-acetylalanine"
FT                   /evidence="ECO:0007744|PubMed:22223895"
FT   HELIX           66..73
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   STRAND          77..85
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   STRAND          88..94
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   HELIX           105..111
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   TURN            114..116
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   STRAND          121..128
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   STRAND          134..141
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   HELIX           151..164
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   STRAND          175..177
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   STRAND          180..186
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   STRAND          192..195
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   HELIX           203..205
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   STRAND          220..225
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   STRAND          228..247
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   HELIX           255..257
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   HELIX           260..268
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   STRAND          278..286
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   STRAND          289..296
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   TURN            297..299
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   HELIX           306..318
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   STRAND          324..330
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   STRAND          333..339
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   TURN            341..343
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   STRAND          346..350
FT                   /evidence="ECO:0007829|PDB:3EJX"
FT   STRAND          353..361
FT                   /evidence="ECO:0007829|PDB:3EJX"
SQ   SEQUENCE   362 AA;  38984 MW;  B2C18C4714BAA543 CRC64;
     MEIAAVSTVS VAPQSRRVSN AFSRNLGSVS SLSFGFFEKE YCFKSPSLRV SAAASMDAVT
     AEKFSPASFL DKKETGVLHF VKYHGLGNDF ILVDNRDSSE PKITQEQAAK LCDRNFGVGA
     DGVIFAMPGV NGTDYAMRIF NSDGSEPEMC GNGVRCFARF IAELENLQGK HSFTIHTGAG
     LIVPEIQDDG QVKVDMGTPI LKAQDVPTKL SGNKGEAVVE AELVVDGVSW NVTCVSMGNP
     HCITFGKKGG PNLKVDDLNL PEIGPKFEHH EMFPARTNTE FVEVLSRSHL KMRVWERGAG
     ATLACGTGAC ALVVAAVLEG RADRKCTVDL PGGPLEIEWK QEDNHIYMTG PAEAVFYGSA
     LL
//