ID Q39RB7_GEOMG Unreviewed; 282 AA.
AC Q39RB7;
DT 22-NOV-2005, integrated into UniProtKB/TrEMBL.
DT 22-NOV-2005, sequence version 1.
DT 27-MAR-2024, entry version 117.
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:ABB33207.1};
GN OrderedLocusNames=Gmet_2992 {ECO:0000313|EMBL:ABB33207.1};
OS Geobacter metallireducens (strain ATCC 53774 / DSM 7210 / GS-15).
OC Bacteria; Thermodesulfobacteriota; Desulfuromonadia; Geobacterales;
OC Geobacteraceae; Geobacter.
OX NCBI_TaxID=269799 {ECO:0000313|EMBL:ABB33207.1, ECO:0000313|Proteomes:UP000007073};
RN [1] {ECO:0000313|EMBL:ABB33207.1, ECO:0000313|Proteomes:UP000007073}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 53774 / DSM 7210 / GS-15
RC {ECO:0000313|Proteomes:UP000007073};
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T.,
RA Hammon N., Israni S., Pitluck S., Di Bartolo G., Chain P., Schmutz J.,
RA Larimer F., Land M., Kyrpides N., Ivanova N., Richardson P.;
RT "Complete sequence of Geobacter metallireducens GS-15.";
RL Submitted (OCT-2005) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:ABB33207.1, ECO:0000313|Proteomes:UP000007073}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 53774 / DSM 7210 / GS-15
RC {ECO:0000313|Proteomes:UP000007073};
RX PubMed=19473543; DOI=10.1186/1471-2180-9-109;
RA Aklujkar M., Krushkal J., DiBartolo G., Lapidus A., Land M.L., Lovley D.R.;
RT "The genome sequence of Geobacter metallireducens: features of metabolism,
RT physiology and regulation common and dissimilar to Geobacter
RT sulfurreducens.";
RL BMC Microbiol. 9:109-109(2009).
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}.
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DR EMBL; CP000148; ABB33207.1; -; Genomic_DNA.
DR RefSeq; WP_004514483.1; NC_007517.1.
DR AlphaFoldDB; Q39RB7; -.
DR STRING; 269799.Gmet_2992; -.
DR KEGG; gme:Gmet_2992; -.
DR eggNOG; COG0253; Bacteria.
DR HOGENOM; CLU_053306_3_0_7; -.
DR UniPathway; UPA00034; UER00025.
DR Proteomes; UP000007073; 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 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:UP000007073}.
FT ACT_SITE 71
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU10125"
FT ACT_SITE 71
FT /note="Proton donor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT ACT_SITE 223
FT /note="Proton acceptor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 11
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 62
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 72..73
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 163
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 196
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00197"
FT BINDING 214..215
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 SITE 165
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 214
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 282 AA; 30849 MW; 4DF6313049864BA5 CRC64;
MKFTKMHGAG NDYVYVNCFE ERVDNPEQVA IKVSNRNFGI GSDGLILIMP SDKADVRMRM
FNSDGSESEM CGNGIRCVAK YAYDHGIVSK KEITAETGAG ILTLQLVPGA DGKIEKVRVN
MGVPRLKRAE IPMAGEPADG QIVSQPLNIL HTTFNITCVS MGNPHCVIFV DDVESFQVEK
YGPLIENHEL FPRRTNVEFV QIISRTEVRQ RTWERGAGET LACGTGASAV CVAGALNCLT
EKKILNHLSG GDLELEWADD GFLYMTGPAT EVFSGEIDLA KL
//
