DAPF_ARATH
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 03-AUG-2022, entry version 121.
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.AT3G53580.1; -.
DR iPTMnet; Q9LFG2; -.
DR MetOSite; Q9LFG2; -.
DR PaxDb; Q9LFG2; -.
DR PRIDE; Q9LFG2; -.
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; locus:2084011; AT3G53580.
DR eggNOG; ENOG502QQKJ; Eukaryota.
DR HOGENOM; CLU_053306_2_1_1; -.
DR InParanoid; Q9LFG2; -.
DR OMA; IYARYLF; -.
DR OrthoDB; 1209512at2759; -.
DR PhylomeDB; Q9LFG2; -.
DR BioCyc; ARA:AT3G53580-MON; -.
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 Genevisible; Q9LFG2; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0008837; F:diaminopimelate epimerase activity; IBA:GO_Central.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IBA:GO_Central.
DR HAMAP; MF_00197; DAP_epimerase; 1.
DR InterPro; IPR018510; DAP_epimerase_AS.
DR InterPro; IPR001653; DAP_epimerase_DapF.
DR PANTHER; PTHR31689; PTHR31689; 1.
DR Pfam; PF01678; DAP_epimerase; 2.
DR TIGRFAMs; TIGR00652; DapF; 1.
DR PROSITE; PS01326; DAP_EPIMERASE; 1.
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
