DAPF_THEMA
ID DAPF_THEMA Reviewed; 236 AA.
AC Q9X1L0; G4FFQ9;
DT 11-DEC-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 131.
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, ECO:0000269|PubMed:30548096};
DE AltName: Full=Dpm epimerase {ECO:0000303|PubMed:30548096};
DE AltName: Full=PLP-independent amino acid racemase {ECO:0000255|HAMAP-Rule:MF_00197};
GN Name=dapF {ECO:0000255|HAMAP-Rule:MF_00197};
GN OrderedLocusNames=TM_1522 {ECO:0000312|EMBL:AAD36589.1};
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY, AND
RP SUBUNIT.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=30548096; DOI=10.1111/febs.14720;
RA Miyamoto T., Katane M., Saitoh Y., Sekine M., Homma H.;
RT "Elucidation of the D-lysine biosynthetic pathway in the hyperthermophile
RT Thermotoga maritima.";
RL FEBS J. 286:601-614(2019).
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 (PubMed:30548096). Also catalyzes the racemization of certain amino
CC acids, including Lys, with low efficiency (PubMed:30548096).
CC {ECO:0000269|PubMed:30548096}.
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, ECO:0000269|PubMed:30548096};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.082 mM for L,L-DAP {ECO:0000269|PubMed:30548096};
CC KM=0.258 mM for meso-DAP {ECO:0000269|PubMed:30548096};
CC KM=594 mM for L-Lys {ECO:0000269|PubMed:30548096};
CC KM=619 mM for D-Lys {ECO:0000269|PubMed:30548096};
CC Vmax=1.87 umol/sec/mg enzyme with L,L-DAP as substrate
CC {ECO:0000269|PubMed:30548096};
CC Vmax=2.63 umol/sec/mg enzyme with meso-DAP as substrate
CC {ECO:0000269|PubMed:30548096};
CC Vmax=0.34 umol/sec/mg enzyme with L-Lys as substrate
CC {ECO:0000269|PubMed:30548096};
CC Vmax=0.37 umol/sec/mg enzyme with D-Lys as substrate
CC {ECO:0000269|PubMed:30548096};
CC Note=kcat is 56.2 sec(-1) with L,L-DAP as substrate. kcat is 79.1
CC sec(-1) with meso-DAP as substrate. kcat is 10.1 sec(-1) with L-Lys
CC as substrate. kcat is 11.2 sec(-1) with D-Lys as substrate.
CC {ECO:0000269|PubMed:30548096};
CC pH dependence:
CC Optimum pH is 7.5-8.0. {ECO:0000269|PubMed:30548096};
CC Temperature dependence:
CC Optimum temperature is 90 degrees Celsius.
CC {ECO:0000269|PubMed:30548096};
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, ECO:0000305|PubMed:30548096}.
CC -!- SUBUNIT: Probably forms homotrimers. {ECO:0000269|PubMed:30548096}.
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; AE000512; AAD36589.1; -; Genomic_DNA.
DR PIR; C72246; C72246.
DR RefSeq; NP_229322.1; NC_000853.1.
DR RefSeq; WP_004081881.1; NZ_CP011107.1.
DR AlphaFoldDB; Q9X1L0; -.
DR SMR; Q9X1L0; -.
DR STRING; 243274.THEMA_06690; -.
DR DNASU; 897985; -.
DR EnsemblBacteria; AAD36589; AAD36589; TM_1522.
DR KEGG; tma:TM1522; -.
DR PATRIC; fig|243274.17.peg.1530; -.
DR InParanoid; Q9X1L0; -.
DR OMA; CGNGART; -.
DR OrthoDB; 1921631at2; -.
DR UniPathway; UPA00034; UER00025.
DR Proteomes; UP000008183; 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 1: Evidence at protein level;
KW Amino-acid biosynthesis; Cytoplasm; Isomerase; Lysine biosynthesis;
KW Reference proteome.
FT CHAIN 1..236
FT /note="Diaminopimelate epimerase"
FT /id="PRO_0000448681"
FT ACT_SITE 64
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT ACT_SITE 186
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 8
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 55
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 65..66
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 159
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 176..177
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 187..188
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT SITE 132
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 176
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 236 AA; 26874 MW; A14E28EF7AEAE201 CRC64;
MCYSANGNTF LIVDNTQKRI PEEKKPDFVR ENVGDLDGVI FVELVDGKYF MDYYNRDGSM
AAFCGNGARA FSQYLIDRGW IKEKEFTFLS RAGEIKVIVD DSIWVRMPGV SEKKEMKVDG
YEGYFVVVGV PHFVMEVKGI DELDVEKLGR DLRYKTGANV DFYEVLPDRL KVRTYERGVE
RETKACGTGV TSVFVVYRDK TGAKEVKIQV PGGTLFLKEE NGEIFLRGDV KRCSEE
