ID D4BND6_BIFBR Unreviewed; 299 AA.
AC D4BND6;
DT 18-MAY-2010, integrated into UniProtKB/TrEMBL.
DT 18-MAY-2010, sequence version 1.
DT 24-JAN-2024, entry version 61.
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:EFE89173.1};
GN ORFNames=BIFBRE_03585 {ECO:0000313|EMBL:EFE89173.1};
OS Bifidobacterium breve DSM 20213 = JCM 1192.
OC Bacteria; Actinomycetota; Actinomycetes; Bifidobacteriales;
OC Bifidobacteriaceae; Bifidobacterium.
OX NCBI_TaxID=518634 {ECO:0000313|EMBL:EFE89173.1, ECO:0000313|Proteomes:UP000003191};
RN [1] {ECO:0000313|EMBL:EFE89173.1, ECO:0000313|Proteomes:UP000003191}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 20213 {ECO:0000313|EMBL:EFE89173.1,
RC ECO:0000313|Proteomes:UP000003191};
RA Weinstock G., Sodergren E., Clifton S., Fulton L., Fulton B., Courtney L.,
RA Fronick C., Harrison M., Strong C., Farmer C., Delahaunty K., Markovic C.,
RA Hall O., Minx P., Tomlinson C., Mitreva M., Nelson J., Hou S., Wollam A.,
RA Pepin K.H., Johnson M., Bhonagiri V., Zhang X., Suruliraj S., Warren W.,
RA Chinwalla A., Mardis E.R., Wilson R.K.;
RL Submitted (FEB-2010) 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: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}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_00197}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:EFE89173.1}.
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DR EMBL; ACCG02000009; EFE89173.1; -; Genomic_DNA.
DR RefSeq; WP_003828721.1; NZ_JDUD01000004.1.
DR AlphaFoldDB; D4BND6; -.
DR STRING; 1685.RY69_1351; -.
DR PATRIC; fig|518634.7.peg.669; -.
DR HOGENOM; CLU_053306_4_0_11; -.
DR UniPathway; UPA00034; UER00025.
DR Proteomes; UP000003191; Unassembled WGS sequence.
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}; Reference proteome {ECO:0000313|Proteomes:UP000003191}.
FT ACT_SITE 91
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU10125"
FT ACT_SITE 91
FT /note="Proton donor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT ACT_SITE 244
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 15
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 82
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 92..93
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 174
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 211
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 235..236
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 245..246
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT SITE 176
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 235
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"
SQ SEQUENCE 299 AA; 32346 MW; ECC0304AECA07B35 CRC64;
MSLPQRVTKT HATGNDFVVY LDKTGDFEPT ADEIRFLCDR HFGIGGDGLI RLTKPEFVSD
LSDEQIMAVQ AGDAEWFMDY RNADGSLAEM CGNGTRAITL FAQREGVADS TEPFRLGTRA
GVKILTPRGN VKPYGANVFQ VEMGEWKIGE TDAYEVTIPG NDGSARGTFV DMGNPHVVAV
IEDAFSTLPV VEDLDLVTKP VVNPTIESDQ NVEFVRIDDI DHNTAVGEAT MRVNERGCGE
TLSCGTGLCA TGIVLRAKTG ISHWDITVRG GTLRVDVTDE DVKLTGSATL VADIDLLRS
//
