ID   DAPF_PSEMY              Reviewed;         276 AA.
AC   A4XNX4;
DT   15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT   29-MAY-2007, sequence version 1.
DT   27-MAR-2024, entry version 91.
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=Pmen_0266;
OS   Pseudomonas mendocina (strain ymp).
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales;
OC   Pseudomonadaceae; Pseudomonas.
OX   NCBI_TaxID=399739;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ymp;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E.,
RA   Tice H., Pitluck S., Kiss H., Brettin T., Detter J.C., Bruce D., Han C.,
RA   Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N.,
RA   Hersman L., Dubois J., Maurice P., Richardson P.;
RT   "Complete sequence of Pseudomonas mendocina ymp.";
RL   Submitted (APR-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; CP000680; ABP83040.1; -; Genomic_DNA.
DR   AlphaFoldDB; A4XNX4; -.
DR   SMR; A4XNX4; -.
DR   STRING; 399739.Pmen_0266; -.
DR   KEGG; pmy:Pmen_0266; -.
DR   PATRIC; fig|399739.8.peg.272; -.
DR   eggNOG; COG0253; Bacteria.
DR   HOGENOM; CLU_053306_1_1_6; -.
DR   OrthoDB; 9805408at2; -.
DR   UniPathway; UPA00034; UER00025.
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.
FT   CHAIN           1..276
FT                   /note="Diaminopimelate epimerase"
FT                   /id="PRO_1000011934"
FT   ACT_SITE        75
FT                   /note="Proton donor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   ACT_SITE        219
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         13
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         46
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         66
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         76..77
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         159
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         192
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         210..211
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         220..221
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   SITE            161
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            210
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            270
FT                   /note="Important for dimerization"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
SQ   SEQUENCE   276 AA;  30436 MW;  3F10B1214260EAC7 CRC64;
     MLLRFTKMHG LGNDFMVLDL ISQHAHVQPK HAKQWGDRHT GVGFDQLLIV EPPSHPDVDF
     RYRIFNSDGS EVEQCGNGAR CFARFVLDKR LTTKKTIRVE TKSGVIELRV QNDGQVCVNM
     GAPRLEPAQV PFQAEQAALT YRVDVEGQSV ELAALSMGNP HAVLRVDNVD SAPVHTLGPK
     LEHHPRFPQR VNVGFLQVLD RKHARLRVWE RGAGETQACG TGACAAAVAA IRQGWMDSPV
     QLELPGGKLS IEWAGEGQPV MMTGPAARVY EGQVRL
//