ID   DAPF_METC4              Reviewed;         296 AA.
AC   B7KQM2;
DT   28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   10-FEB-2009, sequence version 1.
DT   03-AUG-2022, entry version 67.
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}; OrderedLocusNames=Mchl_2947;
OS   Methylorubrum extorquens (strain CM4 / NCIMB 13688) (Methylobacterium
OS   extorquens).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC   Methylobacteriaceae; Methylorubrum.
OX   NCBI_TaxID=440085;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CM4 / NCIMB 13688;
RG   US DOE Joint Genome Institute;
RA   Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA   Bruce D., Goodwin L., Pitluck S., Chertkov O., Brettin T., Detter J.C.,
RA   Han C., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N.,
RA   Marx C., Richardson P.;
RT   "Complete sequence of chromosome of Methylobacterium chloromethanicum
RT   CM4.";
RL   Submitted (DEC-2008) 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; CP001298; ACK83786.1; -; Genomic_DNA.
DR   RefSeq; WP_015951208.1; NC_011757.1.
DR   AlphaFoldDB; B7KQM2; -.
DR   SMR; B7KQM2; -.
DR   EnsemblBacteria; ACK83786; ACK83786; Mchl_2947.
DR   KEGG; mch:Mchl_2947; -.
DR   HOGENOM; CLU_053306_1_0_5; -.
DR   OMA; HVAMRVH; -.
DR   BioCyc; MEXT440085:MCHL_RS14335-MON; -.
DR   UniPathway; UPA00034; UER00025.
DR   Proteomes; UP000002385; 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   PANTHER; PTHR31689; PTHR31689; 1.
DR   Pfam; PF01678; DAP_epimerase; 2.
DR   TIGRFAMs; TIGR00652; DapF; 1.
DR   PROSITE; PS01326; DAP_EPIMERASE; 1.
PE   3: Inferred from homology;
KW   Amino-acid biosynthesis; Cytoplasm; Isomerase; Lysine biosynthesis.
FT   CHAIN           1..296
FT                   /note="Diaminopimelate epimerase"
FT                   /id="PRO_1000124420"
FT   ACT_SITE        78
FT                   /note="Proton donor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   ACT_SITE        232
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         17
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         49
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         69
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         79..80
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         171
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   BINDING         205
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   BINDING         233..234
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT   SITE            173
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            223
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"
SQ   SEQUENCE   296 AA;  31877 MW;  F01A444D94EAD5F3 CRC64;
     MSPLANRRFL KMHGAGNAIV VLDLRGTAVR VTPAEARAIA ADVHSRFDQL MVVHDPVTPG
     TDAFMRIYNT DGSESGACGN GTRCVGYALL DDPAMARPAE NGALTLETKA GLVAVKRITE
     RSFTVDMGQP RLRWDEIPLT EPFLDTRRIE LQVGPIDDPI LHSPAAVSMG NPHAIFFVER
     DPDSYDLGRI GPLLEAHPIF PERANISIAE VTSRDTIKLR VWERGAGLTL ACGTAACATV
     VAASRLRMIG RAARVALPGG ELSIEWRADD HVLMTGPVYL EGEGTFSPDL FAGIDG