ID C3LPW8_VIBCM Unreviewed; 290 AA.
AC C3LPW8;
DT 16-JUN-2009, integrated into UniProtKB/TrEMBL.
DT 16-JUN-2009, sequence version 1.
DT 27-MAR-2024, entry version 86.
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:ACP04462.1};
GN OrderedLocusNames=VCM66_0126 {ECO:0000313|EMBL:ACP04462.1};
OS Vibrio cholerae serotype O1 (strain M66-2).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=579112 {ECO:0000313|EMBL:ACP04462.1, ECO:0000313|Proteomes:UP000001217};
RN [1] {ECO:0000313|EMBL:ACP04462.1, ECO:0000313|Proteomes:UP000001217}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=M66-2 {ECO:0000313|EMBL:ACP04462.1,
RC ECO:0000313|Proteomes:UP000001217};
RX PubMed=19115014; DOI=10.1371/journal.pone.0004053;
RA Feng L., Reeves P.R., Lan R., Ren Y., Gao C., Zhou Z., Ren Y., Cheng J.,
RA Wang W., Wang J., Qian W., Li D., Wang L.;
RT "A recalibrated molecular clock and independent origins for the cholera
RT pandemic clones.";
RL PLoS ONE 3:E4053-E4053(2008).
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; CP001233; ACP04462.1; -; Genomic_DNA.
DR AlphaFoldDB; C3LPW8; -.
DR KEGG; vcm:VCM66_0126; -.
DR HOGENOM; CLU_053306_1_1_6; -.
DR UniPathway; UPA00034; UER00025.
DR Proteomes; UP000001217; Chromosome I.
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 {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 89
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU10125"
FT ACT_SITE 89
FT /note="Proton donor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT ACT_SITE 233
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 27
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 60
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 80
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 90..91
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 173
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 206
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 224..225
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 234..235
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT SITE 175
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 224
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 284
FT /note="Important for dimerization"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
SQ SEQUENCE 290 AA; 32051 MW; 26C4EDD400A410AC CRC64;
MGVRIGITGV KLSSMHFHFS KMHGLGNDFM VVDCITQNVF FSPELIRRLA DRHTGVGFDQ
LLVVEAPYDP ESDFHYRIFN ADGSEVEQCG NGARCFARFV RMKGLTNKYT IHVSTKKGKM
VLNVEEEDLI TVNMGVPEFE PNKIPFRAKQ SEKTYILRVG EHTLFCGAVS MGNPHVVTVV
DDIRTAAVET LGPLLESHER FPERVNAGFM QVVSRDEINL RVYERGAGET QACGSGACAA
VAVGILQGLL DEQVRVHLPG GELEIHWQGP GKPLYMTGPA THIYDGQISC
//
