ID C4K4D9_HAMD5 Unreviewed; 278 AA.
AC C4K4D9;
DT 07-JUL-2009, integrated into UniProtKB/TrEMBL.
DT 07-JUL-2009, sequence version 1.
DT 27-MAR-2024, entry version 81.
DE RecName: Full=Diaminopimelate epimerase {ECO:0000256|ARBA:ARBA00013080, ECO:0000256|HAMAP-Rule:MF_00197};
DE Short=DAP epimerase {ECO:0000256|HAMAP-Rule:MF_00197};
DE EC=5.1.1.7 {ECO:0000256|ARBA:ARBA00013080, ECO:0000256|HAMAP-Rule:MF_00197};
DE AltName: Full=PLP-independent amino acid racemase {ECO:0000256|HAMAP-Rule:MF_00197};
GN Name=dapF {ECO:0000256|HAMAP-Rule:MF_00197,
GN ECO:0000313|EMBL:ACQ67432.1};
GN OrderedLocusNames=HDEF_0699 {ECO:0000313|EMBL:ACQ67432.1};
OS Hamiltonella defensa subsp. Acyrthosiphon pisum (strain 5AT).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; aphid secondary symbionts; Hamiltonella.
OX NCBI_TaxID=572265 {ECO:0000313|EMBL:ACQ67432.1, ECO:0000313|Proteomes:UP000002334};
RN [1] {ECO:0000313|EMBL:ACQ67432.1, ECO:0000313|Proteomes:UP000002334}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=5AT {ECO:0000313|Proteomes:UP000002334};
RX PubMed=19451630; DOI=10.1073/pnas.0900194106;
RA Degnan P.H., Yu Y., Sisneros N., Wing R.A., Moran N.A.;
RT "Hamiltonella defensa, genome evolution of protective bacterial
RT endosymbiont from pathogenic ancestors.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:9063-9068(2009).
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:0000256|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;
CC Evidence={ECO:0000256|ARBA:ARBA00000599, ECO:0000256|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:0000256|ARBA:ARBA00005196, ECO:0000256|HAMAP-Rule:MF_00197}.
CC -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_00197}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00197}.
CC -!- SIMILARITY: Belongs to the diaminopimelate epimerase family.
CC {ECO:0000256|ARBA:ARBA00010219, ECO:0000256|HAMAP-Rule:MF_00197}.
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DR EMBL; CP001277; ACQ67432.1; -; Genomic_DNA.
DR RefSeq; WP_015873253.1; NC_012751.1.
DR AlphaFoldDB; C4K4D9; -.
DR STRING; 572265.HDEF_0699; -.
DR GeneID; 66260555; -.
DR KEGG; hde:HDEF_0699; -.
DR eggNOG; COG0253; Bacteria.
DR HOGENOM; CLU_053306_1_1_6; -.
DR UniPathway; UPA00034; UER00025.
DR Proteomes; UP000002334; 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 {ECO:0000256|ARBA:ARBA00022605, ECO:0000256|HAMAP-
KW Rule:MF_00197}; Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00197};
KW Isomerase {ECO:0000256|ARBA:ARBA00023235, ECO:0000256|HAMAP-Rule:MF_00197};
KW Lysine biosynthesis {ECO:0000256|ARBA:ARBA00023154, ECO:0000256|HAMAP-
KW Rule:MF_00197}.
FT ACT_SITE 73
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU10125"
FT ACT_SITE 73
FT /note="Proton donor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT ACT_SITE 217
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 11
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 44
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 64
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 74..75
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 157
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 190
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 208..209
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 218..219
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT SITE 159
FT /note="Could be important to modulate the pK values of the
FT two catalytic cysteine residues"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT SITE 208
FT /note="Could be important to modulate the pK values of the
FT two catalytic cysteine residues"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT SITE 268
FT /note="Important for dimerization"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
SQ SEQUENCE 278 AA; 31008 MW; 48021B32ACAC0E05 CRC64;
MRFSKMCSLG NDFVIIDAVT QNVHLRSEFI CRLANRHTGI GFDQLLLLEP PNSPELDFHY
RIFNADGSEV FQCGNGARCL GRFVHLKGLT NKKNIQVSTK TVKMQIHLEE KNQICVNMGE
PDFFPQTIPF RSKTIKKIYE LDVAEQKLLC GIVSMGNPHC IIQVEKLDSD QIKLIGPLLG
CHPSFPEGTN VGFMQIIDRK HIHLRVYERG AGETQACGSG ACAAVSIGVQ QDLLDEKVHV
EQKGGNLDIC WKGTGHCLYM TGPADHVYDG VIHMSFKP
//
