ID   DAPF_XYLFA              Reviewed;         284 AA.
AC   Q9PD98;
DT   06-JUN-2002, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2000, sequence version 1.
DT   27-MAR-2024, entry version 112.
DE   RecName: Full=Diaminopimelate epimerase {ECO:0000255|HAMAP-Rule:MF_00197};
DE            Short=DAP epimerase {ECO:0000255|HAMAP-Rule:MF_00197};
DE            EC=5.1.1.7 {ECO:0000255|HAMAP-Rule:MF_00197};
DE   AltName: Full=PLP-independent amino acid racemase {ECO:0000255|HAMAP-Rule:MF_00197};
GN   Name=dapF {ECO:0000255|HAMAP-Rule:MF_00197};
GN   OrderedLocusNames=XF_1481;
OS   Xylella fastidiosa (strain 9a5c).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Xanthomonadales;
OC   Xanthomonadaceae; Xylella.
OX   NCBI_TaxID=160492;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=9a5c;
RX   PubMed=10910347; DOI=10.1038/35018003;
RA   Simpson A.J.G., Reinach F.C., Arruda P., Abreu F.A., Acencio M.,
RA   Alvarenga R., Alves L.M.C., Araya J.E., Baia G.S., Baptista C.S.,
RA   Barros M.H., Bonaccorsi E.D., Bordin S., Bove J.M., Briones M.R.S.,
RA   Bueno M.R.P., Camargo A.A., Camargo L.E.A., Carraro D.M., Carrer H.,
RA   Colauto N.B., Colombo C., Costa F.F., Costa M.C.R., Costa-Neto C.M.,
RA   Coutinho L.L., Cristofani M., Dias-Neto E., Docena C., El-Dorry H.,
RA   Facincani A.P., Ferreira A.J.S., Ferreira V.C.A., Ferro J.A., Fraga J.S.,
RA   Franca S.C., Franco M.C., Frohme M., Furlan L.R., Garnier M., Goldman G.H.,
RA   Goldman M.H.S., Gomes S.L., Gruber A., Ho P.L., Hoheisel J.D.,
RA   Junqueira M.L., Kemper E.L., Kitajima J.P., Krieger J.E., Kuramae E.E.,
RA   Laigret F., Lambais M.R., Leite L.C.C., Lemos E.G.M., Lemos M.V.F.,
RA   Lopes S.A., Lopes C.R., Machado J.A., Machado M.A., Madeira A.M.B.N.,
RA   Madeira H.M.F., Marino C.L., Marques M.V., Martins E.A.L., Martins E.M.F.,
RA   Matsukuma A.Y., Menck C.F.M., Miracca E.C., Miyaki C.Y.,
RA   Monteiro-Vitorello C.B., Moon D.H., Nagai M.A., Nascimento A.L.T.O.,
RA   Netto L.E.S., Nhani A. Jr., Nobrega F.G., Nunes L.R., Oliveira M.A.,
RA   de Oliveira M.C., de Oliveira R.C., Palmieri D.A., Paris A., Peixoto B.R.,
RA   Pereira G.A.G., Pereira H.A. Jr., Pesquero J.B., Quaggio R.B.,
RA   Roberto P.G., Rodrigues V., de Rosa A.J.M., de Rosa V.E. Jr., de Sa R.G.,
RA   Santelli R.V., Sawasaki H.E., da Silva A.C.R., da Silva A.M.,
RA   da Silva F.R., Silva W.A. Jr., da Silveira J.F., Silvestri M.L.Z.,
RA   Siqueira W.J., de Souza A.A., de Souza A.P., Terenzi M.F., Truffi D.,
RA   Tsai S.M., Tsuhako M.H., Vallada H., Van Sluys M.A., Verjovski-Almeida S.,
RA   Vettore A.L., Zago M.A., Zatz M., Meidanis J., Setubal J.C.;
RT   "The genome sequence of the plant pathogen Xylella fastidiosa.";
RL   Nature 406:151-159(2000).
CC   -!- FUNCTION: Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate
CC       (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-
CC       lysine and an essential component of the bacterial peptidoglycan.
CC       {ECO:0000255|HAMAP-Rule:MF_00197}.
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; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00197};
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       {ECO:0000255|HAMAP-Rule:MF_00197}.
CC   -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00197}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00197}.
CC   -!- SIMILARITY: Belongs to the diaminopimelate epimerase family.
CC       {ECO:0000255|HAMAP-Rule:MF_00197}.
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DR   EMBL; AE003849; AAF84290.1; -; Genomic_DNA.
DR   PIR; D82677; D82677.
DR   RefSeq; WP_010893982.1; NC_002488.3.
DR   AlphaFoldDB; Q9PD98; -.
DR   SMR; Q9PD98; -.
DR   STRING; 160492.XF_1481; -.
DR   KEGG; xfa:XF_1481; -.
DR   eggNOG; COG0253; Bacteria.
DR   HOGENOM; CLU_053306_1_1_6; -.
DR   UniPathway; UPA00034; UER00025.
DR   Proteomes; UP000000812; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0008837; F:diaminopimelate epimerase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniRule.
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.
PE   3: Inferred from homology;
KW   Amino-acid biosynthesis; Cytoplasm; Isomerase; Lysine biosynthesis.
FT   CHAIN           1..284
FT                   /note="Diaminopimelate epimerase"
FT                   /id="PRO_0000149882"
FT   ACT_SITE        82
FT                   /note="Proton donor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   ACT_SITE        227
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         20
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         53
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         73
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         83..84
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         167
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         200
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         218..219
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         228..229
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   SITE            169
FT                   /note="Could be important to modulate the pK values of the
FT                   two catalytic cysteine residues"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   SITE            218
FT                   /note="Could be important to modulate the pK values of the
FT                   two catalytic cysteine residues"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   SITE            278
FT                   /note="Important for dimerization"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
SQ   SEQUENCE   284 AA;  30123 MW;  AFB170A1E437D918 CRC64;
     MGVESVRCPL HFTKMQGAGN DFVVLDLRDG TPPPDVALVA WLADRHFGIG CDQVIAIEPP
     RGVGVFAAYR IWNADGSAAQ QCGNGARCVA AWLVRDGSVA DEHFLIDSPV QAHLVRCIGK
     DEYAVEMGLP VFEPERIPLS GFPNACGEYV LSLQGEVLRC GAVSMGNPHA VVEVDLIDVA
     PVERIGSLLQ QHVAFPESVN VGFVQVIDPG LVRLRVYERG AGETLACGSG ACAAAVVLMQ
     RGRVGRDVRV VLPGGTLRVQ WPVSGGPVTL SGPAKCVFDG VWYG
//