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Diaminopimelate epimerase, chloroplastic (DAP epimerase) (EC 5.1.1.7)

 DAPF_ARATH              Reviewed;         362 AA.
Q9LFG2;
23-OCT-2007, integrated into UniProtKB/Swiss-Prot.
01-OCT-2000, sequence version 1.
25-APR-2018, entry version 102.
RecName: Full=Diaminopimelate epimerase, chloroplastic;
Short=DAP epimerase;
EC=5.1.1.7;
Flags: Precursor;
Name=DAPF; OrderedLocusNames=At3g53580; ORFNames=F4P12.280;
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=11130713; DOI=10.1038/35048706;
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.;
"Sequence and analysis of chromosome 3 of the plant Arabidopsis
thaliana.";
Nature 408:820-822(2000).
[2]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
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.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[4]
FUNCTION.
PubMed=15652176; DOI=10.1016/j.bbagen.2004.09.008;
Hudson A.O., Bless C., Macedo P., Chatterjee S.P., Singh B.K.,
Gilvarg C., Leustek T.;
"Biosynthesis of lysine in plants: evidence for a variant of the known
bacterial pathways.";
Biochim. Biophys. Acta 1721:27-36(2005).
[5]
ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-53, CLEAVAGE OF TRANSIT
PEPTIDE [LARGE SCALE ANALYSIS] AFTER ALA-52, AND IDENTIFICATION BY
MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22223895; DOI=10.1074/mcp.M111.015131;
Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C.,
Meinnel T., Giglione C.;
"Comparative large-scale characterisation of plant vs. mammal proteins
reveals similar and idiosyncratic N-alpha acetylation features.";
Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
[6]
X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) OF 52-362 IN COMPLEX WITH
INHIBITORS.
PubMed=19013471; DOI=10.1016/j.jmb.2008.10.072;
Pillai B., Moorthie V.A., van Belkum M.J., Marcus S.L., Cherney M.M.,
Diaper C.M., Vederas J.C., James M.N.;
"Crystal structure of diaminopimelate epimerase from Arabidopsis
thaliana, an amino acid racemase critical for L-lysine biosynthesis.";
J. Mol. Biol. 385:580-594(2009).
-!- FUNCTION: 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.
{ECO:0000269|PubMed:15652176}.
-!- CATALYTIC ACTIVITY: LL-2,6-diaminoheptanedioate = meso-
diaminoheptanedioate.
-!- ENZYME REGULATION: Inhibited by aziridino-diaminopimelate
(AziDAP).
-!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step
1/1.
-!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}.
-!- MISCELLANEOUS: This enzyme requires no cofactors.
-!- SIMILARITY: Belongs to the diaminopimelate epimerase family.
{ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AL132966; CAB67665.1; -; Genomic_DNA.
EMBL; CP002686; AEE79113.1; -; Genomic_DNA.
EMBL; AY126996; AAM83223.1; -; mRNA.
EMBL; AY143871; AAN28810.1; -; mRNA.
PIR; T45898; T45898.
RefSeq; NP_190926.1; NM_115218.4.
UniGene; At.21032; -.
PDB; 3EJX; X-ray; 1.95 A; A/B/C/D/E/F=52-362.
PDB; 3EKM; X-ray; 2.30 A; A/B/C/D/E/F=52-362.
PDBsum; 3EJX; -.
PDBsum; 3EKM; -.
ProteinModelPortal; Q9LFG2; -.
SMR; Q9LFG2; -.
BioGrid; 9843; 1.
STRING; 3702.AT3G53580.1; -.
iPTMnet; Q9LFG2; -.
PaxDb; Q9LFG2; -.
PRIDE; Q9LFG2; -.
EnsemblPlants; AT3G53580.1; AT3G53580.1; AT3G53580.
GeneID; 824526; -.
Gramene; AT3G53580.1; AT3G53580.1; AT3G53580.
KEGG; ath:AT3G53580; -.
Araport; AT3G53580; -.
TAIR; locus:2084011; AT3G53580.
eggNOG; ENOG410IHJB; Eukaryota.
eggNOG; COG0253; LUCA.
HOGENOM; HOG000220466; -.
InParanoid; Q9LFG2; -.
KO; K01778; -.
OMA; SMCGNGG; -.
OrthoDB; EOG09360FF0; -.
PhylomeDB; Q9LFG2; -.
BioCyc; ARA:AT3G53580-MONOMER; -.
BRENDA; 5.1.1.7; 399.
UniPathway; UPA00034; UER00025.
EvolutionaryTrace; Q9LFG2; -.
PRO; PR:Q9LFG2; -.
Proteomes; UP000006548; Chromosome 3.
ExpressionAtlas; Q9LFG2; baseline and differential.
Genevisible; Q9LFG2; AT.
GO; GO:0009507; C:chloroplast; IDA:TAIR.
GO; GO:0009570; C:chloroplast stroma; IDA:TAIR.
GO; GO:0005829; C:cytosol; IBA:GO_Central.
GO; GO:0008837; F:diaminopimelate epimerase activity; IBA:GO_Central.
GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IBA:GO_Central.
HAMAP; MF_00197; DAP_epimerase; 1.
InterPro; IPR018510; DAP_epimerase_AS.
InterPro; IPR001653; DAP_epimerase_DapF.
PANTHER; PTHR31689; PTHR31689; 1.
Pfam; PF01678; DAP_epimerase; 2.
TIGRFAMs; TIGR00652; DapF; 1.
PROSITE; PS01326; DAP_EPIMERASE; 1.
1: Evidence at protein level;
3D-structure; Acetylation; Amino-acid biosynthesis; Chloroplast;
Complete proteome; Isomerase; Lysine biosynthesis; Plastid;
Reference proteome; Transit peptide.
TRANSIT 1 52 Chloroplast.
{ECO:0000244|PubMed:22223895,
ECO:0000255}.
CHAIN 53 362 Diaminopimelate epimerase, chloroplastic.
/FTId=PRO_0000307179.
REGION 151 152 Substrate binding.
REGION 296 297 Substrate binding.
REGION 306 307 Substrate binding.
ACT_SITE 150 150
ACT_SITE 305 305
BINDING 88 88 Substrate.
BINDING 141 141 Substrate.
BINDING 239 239 Substrate.
BINDING 278 278 Substrate.
MOD_RES 53 53 N-acetylalanine.
{ECO:0000244|PubMed:22223895}.
HELIX 66 73 {ECO:0000244|PDB:3EJX}.
STRAND 77 85 {ECO:0000244|PDB:3EJX}.
STRAND 88 94 {ECO:0000244|PDB:3EJX}.
HELIX 105 111 {ECO:0000244|PDB:3EJX}.
TURN 114 116 {ECO:0000244|PDB:3EJX}.
STRAND 121 128 {ECO:0000244|PDB:3EJX}.
STRAND 134 141 {ECO:0000244|PDB:3EJX}.
HELIX 151 164 {ECO:0000244|PDB:3EJX}.
STRAND 175 177 {ECO:0000244|PDB:3EJX}.
STRAND 180 186 {ECO:0000244|PDB:3EJX}.
STRAND 192 195 {ECO:0000244|PDB:3EJX}.
HELIX 203 205 {ECO:0000244|PDB:3EJX}.
STRAND 220 225 {ECO:0000244|PDB:3EJX}.
STRAND 228 247 {ECO:0000244|PDB:3EJX}.
HELIX 255 257 {ECO:0000244|PDB:3EJX}.
HELIX 260 268 {ECO:0000244|PDB:3EJX}.
STRAND 278 286 {ECO:0000244|PDB:3EJX}.
STRAND 289 296 {ECO:0000244|PDB:3EJX}.
TURN 297 299 {ECO:0000244|PDB:3EJX}.
HELIX 306 318 {ECO:0000244|PDB:3EJX}.
STRAND 324 330 {ECO:0000244|PDB:3EJX}.
STRAND 333 339 {ECO:0000244|PDB:3EJX}.
TURN 341 343 {ECO:0000244|PDB:3EJX}.
STRAND 346 350 {ECO:0000244|PDB:3EJX}.
STRAND 353 361 {ECO:0000244|PDB:3EJX}.
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


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