DAPF_XYLF2
ID DAPF_XYLF2 Reviewed; 284 AA.
AC B2IA16;
DT 24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT 10-JUN-2008, sequence version 1.
DT 03-AUG-2022, entry version 73.
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=XfasM23_0734;
OS Xylella fastidiosa (strain M23).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;
OC Xanthomonadaceae; Xylella.
OX NCBI_TaxID=405441;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=M23;
RX PubMed=20601474; DOI=10.1128/jb.00651-10;
RA Chen J., Xie G., Han S., Chertkov O., Sims D., Civerolo E.L.;
RT "Whole genome sequences of two Xylella fastidiosa strains (M12 and M23)
RT causing almond leaf scorch disease in California.";
RL J. Bacteriol. 192:4534-4534(2010).
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; CP001011; ACB92175.1; -; Genomic_DNA.
DR RefSeq; WP_012382526.1; NC_010577.1.
DR AlphaFoldDB; B2IA16; -.
DR SMR; B2IA16; -.
DR EnsemblBacteria; ACB92175; ACB92175; XfasM23_0734.
DR GeneID; 58016246; -.
DR KEGG; xfn:XfasM23_0734; -.
DR HOGENOM; CLU_053306_1_1_6; -.
DR OMA; HVAMRVH; -.
DR UniPathway; UPA00034; UER00025.
DR Proteomes; UP000001698; 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..284
FT /note="Diaminopimelate epimerase"
FT /id="PRO_1000099272"
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; 30098 MW; 0FE6DDBD2F9FE82D CRC64;
MGVESVRCPL HFTKMQGAGN DFVVLDLRDG TPPPDAALVA WLADRHFGIG CDQVIAIEPP
RGVGVFAAYR IWNADGSAAQ QCGNGARCVA AWLVRDGSVA TEHFLIDSPV QTHSVRCIGK
DEYAVEMGLP VFEPERIPLS GFPNALGEYV LSLQGEVLCC GAVSMGNPHA VVEVDLIDVA
PVERIGPLLQ QHSAFPESVN VSFVQVIDPG LVRLRVYERG AGETLACGSG ACAAAVVLMQ
RGRVGRDVRV VLPGGTLRVQ WPVSGGPVTL SGPARCVFDG VWYG
