ID   DAPF_SHELP              Reviewed;         279 AA.
AC   A3Q9P7;
DT   15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT   17-APR-2007, sequence version 1.
DT   27-MAR-2024, entry version 104.
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=Shew_0323;
OS   Shewanella loihica (strain ATCC BAA-1088 / PV-4).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Alteromonadales;
OC   Shewanellaceae; Shewanella.
OX   NCBI_TaxID=323850;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC BAA-1088 / PV-4;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA   Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA   Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.,
RA   Hauser L., Kyrpides N., Mikhailova N., Romine M.F., Serres G.,
RA   Fredrickson J., Tiedje J., Richardson P.;
RT   "Complete sequence of Shewanella loihica PV-4.";
RL   Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases.
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; CP000606; ABO22195.1; -; Genomic_DNA.
DR   RefSeq; WP_011864129.1; NC_009092.1.
DR   AlphaFoldDB; A3Q9P7; -.
DR   SMR; A3Q9P7; -.
DR   STRING; 323850.Shew_0323; -.
DR   KEGG; slo:Shew_0323; -.
DR   eggNOG; COG0253; Bacteria.
DR   HOGENOM; CLU_053306_1_1_6; -.
DR   OrthoDB; 9805408at2; -.
DR   UniPathway; UPA00034; UER00025.
DR   Proteomes; UP000001558; 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; 1.
DR   PROSITE; PS01326; DAP_EPIMERASE; 1.
PE   3: Inferred from homology;
KW   Amino-acid biosynthesis; Cytoplasm; Isomerase; Lysine biosynthesis;
KW   Reference proteome.
FT   CHAIN           1..279
FT                   /note="Diaminopimelate epimerase"
FT                   /id="PRO_1000011964"
FT   ACT_SITE        74
FT                   /note="Proton donor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   ACT_SITE        222
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         12
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         45
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         65
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         75..76
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         162
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         195
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         213..214
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         223..224
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   SITE            164
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            213
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            273
FT                   /note="Important for dimerization"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
SQ   SEQUENCE   279 AA;  30657 MW;  58046848EA6CA3F1 CRC64;
     MIHFTKMHGL GNDFMVVDGV TQNVYFSPEQ IKRLADRNFG IGFDQLLLVE PPYDPDLDFH
     YRIFNADGSE VEQCGNGARC FARFVKSKGL INKQKIKVST SSGKMTLRLE RDGSVTVNMG
     IPVLEPSRIP FNAKKAEKTY LLQADMPEGM QTFLCGAVSM GNPHCVLEVD DVANADVERI
     GSLLTKHERF PKGVNVGFMQ VVDANHIKLR VYERGAAETL ACGSGACAAV AVGQLQGKLA
     RRVRVDLPGG SLTINWEGEG KPLWMTGPAE HVYDGQIQQ
//