DAPF_SYNJB
ID DAPF_SYNJB Reviewed; 285 AA.
AC Q2JLR0;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 07-MAR-2006, sequence version 1.
DT 03-AUG-2022, entry version 86.
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=CYB_1371;
OS Synechococcus sp. (strain JA-2-3B'a(2-13)) (Cyanobacteria bacterium
OS Yellowstone B-Prime).
OC Bacteria; Cyanobacteria; Synechococcales; Synechococcaceae; Synechococcus;
OC unclassified Synechococcus.
OX NCBI_TaxID=321332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JA-2-3B'a(2-13);
RX PubMed=18059494; DOI=10.1038/ismej.2007.46;
RA Bhaya D., Grossman A.R., Steunou A.-S., Khuri N., Cohan F.M., Hamamura N.,
RA Melendrez M.C., Bateson M.M., Ward D.M., Heidelberg J.F.;
RT "Population level functional diversity in a microbial community revealed by
RT comparative genomic and metagenomic analyses.";
RL ISME J. 1:703-713(2007).
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; CP000240; ABD02344.1; -; Genomic_DNA.
DR AlphaFoldDB; Q2JLR0; -.
DR SMR; Q2JLR0; -.
DR STRING; 321332.CYB_1371; -.
DR KEGG; cyb:CYB_1371; -.
DR eggNOG; COG0253; Bacteria.
DR HOGENOM; CLU_053306_2_1_3; -.
DR OMA; HVAMRVH; -.
DR UniPathway; UPA00034; UER00025.
DR Proteomes; UP000001938; 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;
KW Reference proteome.
FT CHAIN 1..285
FT /note="Diaminopimelate epimerase"
FT /id="PRO_1000011975"
FT ACT_SITE 77
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT ACT_SITE 228
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 15
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 68
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 78..79
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 165
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 201
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 219..220
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 229..230
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT SITE 167
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 219
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 285 AA; 30949 MW; 73DAB469419A3471 CRC64;
MTPRLSFHKY QGLGNDFILV DNRWQSQPCL SPEEAVALCN RRFGVGADGV IFLLPGQEGA
DFSMRLFNSD GSEAEMCGNG IRCLARFLQD LGIPGRDGAY QIHTLAGRIV PQVRADGLVT
VDMGIPRLLA KQIPTTLVEP DEKVIRQPLA VAGREWRVTA VSMGNPHCVV FLEEEGSLEE
LDLAAVGPLF EHHPAFPERT NTEFVQVLSP TRLRLRVWER GAGATLACGT GACAVLVAAV
LEERAESQAT VELPGGNLEI RWDPSTQHVW MTGPALHVFS GTTAG
