DAPF_BRADU
ID DAPF_BRADU Reviewed; 291 AA.
AC Q89X45;
DT 20-JUN-2003, integrated into UniProtKB/Swiss-Prot.
DT 20-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 96.
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=bll0477;
OS Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 /
OS NBRC 14792 / USDA 110).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Bradyrhizobiaceae; Bradyrhizobium.
OX NCBI_TaxID=224911;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110;
RX PubMed=12597275; DOI=10.1093/dnares/9.6.189;
RA Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S.,
RA Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M.,
RA Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S.;
RT "Complete genomic sequence of nitrogen-fixing symbiotic bacterium
RT Bradyrhizobium japonicum USDA110.";
RL DNA Res. 9:189-197(2002).
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; BA000040; BAC45742.1; -; Genomic_DNA.
DR RefSeq; NP_767117.1; NC_004463.1.
DR RefSeq; WP_011083308.1; NZ_CP011360.1.
DR AlphaFoldDB; Q89X45; -.
DR SMR; Q89X45; -.
DR STRING; 224911.27348725; -.
DR EnsemblBacteria; BAC45742; BAC45742; BAC45742.
DR GeneID; 64020336; -.
DR KEGG; bja:bll0477; -.
DR PATRIC; fig|224911.44.peg.9011; -.
DR eggNOG; COG0253; Bacteria.
DR HOGENOM; CLU_053306_1_0_5; -.
DR InParanoid; Q89X45; -.
DR OMA; HVAMRVH; -.
DR PhylomeDB; Q89X45; -.
DR UniPathway; UPA00034; UER00025.
DR Proteomes; UP000002526; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0008837; F:diaminopimelate epimerase activity; IBA:GO_Central.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IBA:GO_Central.
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..291
FT /note="Diaminopimelate epimerase"
FT /id="PRO_0000149822"
FT ACT_SITE 79
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 17
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 50
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 70
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 80..81
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"
SQ SEQUENCE 291 AA; 31595 MW; 58112A152FA5D6E3 CRC64;
MSALANHAFA KMNGIGNEIV VVDMRDSTAK VTPDDARAVA SAQGGVPYDQ LMVLQKPRLD
GTEAFISIYN NDGSEAGACG NGMRCVVRRI FEKTGQATAT FETAAGLLNA WQGPAPDLYT
VDMGVPKFGW QDIPLAEEFR DTRYIELQIG PIDNPILHSP SVVSMGNPHA IFWVDDVNAY
DLARFGPLLE NHPIFPERAN ITLAHIVDRD HITIRTWERG AGLTRACGSA ACATAVAAAR
LKRAERNVEI TLPGGKLGIE WRERDDHVLM TGTATFEYEG NFDPALFAPA G
