DAPF_ECOLI
ID DAPF_ECOLI Reviewed; 274 AA.
AC P0A6K1; P08885; P78126; Q2M8B5; Q8X8P8;
DT 29-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 29-MAR-2005, sequence version 1.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=Diaminopimelate epimerase {ECO:0000303|PubMed:6378903};
DE Short=DAP epimerase {ECO:0000303|PubMed:6378903};
DE EC=5.1.1.7 {ECO:0000269|PubMed:3042781, ECO:0000269|PubMed:6378903};
DE AltName: Full=PLP-independent amino acid racemase {ECO:0000255|HAMAP-Rule:MF_00197};
GN Name=dapF {ECO:0000303|PubMed:6378903}; OrderedLocusNames=b3809, JW5592;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=3057443; DOI=10.1093/nar/16.21.10367;
RA Richaud C., Printz C.;
RT "Nucleotide sequence of the dapF gene and flanking regions from Escherichia
RT coli K12.";
RL Nucleic Acids Res. 16:10367-10367(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=1379743; DOI=10.1126/science.1379743;
RA Daniels D.L., Plunkett G. III, Burland V.D., Blattner F.R.;
RT "Analysis of the Escherichia coli genome: DNA sequence of the region from
RT 84.5 to 86.5 minutes.";
RL Science 257:771-778(1992).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 259-274.
RC STRAIN=K12;
RX PubMed=2254268; DOI=10.1128/jb.172.12.6973-6980.1990;
RA Colloms S.D., Sykora P., Szatmari G., Sherratt D.J.;
RT "Recombination at ColE1 cer requires the Escherichia coli xerC gene
RT product, a member of the lambda integrase family of site-specific
RT recombinases.";
RL J. Bacteriol. 172:6973-6980(1990).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-8.
RC STRAIN=K12;
RX PubMed=8874804; DOI=10.1016/0300-9084(96)82192-4;
RA Trotot P., Sismeiro O., Vivares C., Glaser P., Bresson-Roy A., Danchin A.;
RT "Comparative analysis of the cya locus in enterobacteria and related Gram-
RT negative facultative anaerobes.";
RL Biochimie 78:277-287(1996).
RN [7]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL
RP PROPERTIES, AND SUBUNIT.
RX PubMed=6378903; DOI=10.1016/s0021-9258(17)47241-3;
RA Wiseman J.S., Nichols J.S.;
RT "Purification and properties of diaminopimelic acid epimerase from
RT Escherichia coli.";
RL J. Biol. Chem. 259:8907-8914(1984).
RN [8]
RP FUNCTION.
RX PubMed=3031013; DOI=10.1128/jb.169.4.1454-1459.1987;
RA Richaud C., Higgins W., Mengin-Lecreulx D., Stragier P.;
RT "Molecular cloning, characterization, and chromosomal localization of dapF,
RT the Escherichia coli gene for diaminopimelate epimerase.";
RL J. Bacteriol. 169:1454-1459(1987).
RN [9]
RP FUNCTION, DISRUPTION PHENOTYPE, AND PATHWAY.
RX PubMed=3283102; DOI=10.1128/jb.170.5.2031-2039.1988;
RA Mengin-Lecreulx D., Michaud C., Richaud C., Blanot D., van Heijenoort J.;
RT "Incorporation of LL-diaminopimelic acid into peptidoglycan of Escherichia
RT coli mutants lacking diaminopimelate epimerase encoded by dapF.";
RL J. Bacteriol. 170:2031-2039(1988).
RN [10]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=3042781; DOI=10.1016/s0021-9258(18)37858-x;
RA Lam L.K., Arnold L.D., Kalantar T.H., Kelland J.G., Lane-Bell P.M.,
RA Palcic M.M., Pickard M.A., Vederas J.C.;
RT "Analogs of diaminopimelic acid as inhibitors of meso-diaminopimelate
RT dehydrogenase and LL-diaminopimelate epimerase.";
RL J. Biol. Chem. 263:11814-11819(1988).
RN [11]
RP ACTIVITY REGULATION.
RX PubMed=2197412; DOI=10.1021/jm00170a018;
RA Gerhart F., Higgins W., Tardif C., Ducep J.B.;
RT "2-(4-Amino-4-carboxybutyl)aziridine-2-carboxylic acid. A potent
RT irreversible inhibitor of diaminopimelic acid epimerase. Spontaneous
RT formation from alpha-(halomethyl)diaminopimelic acids.";
RL J. Med. Chem. 33:2157-2162(1990).
RN [12]
RP PRELIMINARY CRYSTALLIZATION.
RX PubMed=20057066; DOI=10.1107/s1744309109047708;
RA Hor L., Dobson R.C., Dogovski C., Hutton C.A., Perugini M.A.;
RT "Crystallization and preliminary X-ray diffraction analysis of
RT diaminopimelate epimerase from Escherichia coli.";
RL Acta Crystallogr. F 66:37-40(2010).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS), MUTAGENESIS OF TYR-268, AND
RP SUBUNIT.
RX PubMed=23426375; DOI=10.1074/jbc.m113.450148;
RA Hor L., Dobson R.C., Downton M.T., Wagner J., Hutton C.A., Perugini M.A.;
RT "Dimerization of bacterial diaminopimelate epimerase is essential for
RT catalysis.";
RL J. Biol. Chem. 288:9238-9248(2013).
CC -!- FUNCTION: Involved in the succinylase branch of the L-lysine
CC biosynthesis and in the biosynthesis of the pentapeptide incorporated
CC in the peptidoglycan moiety (PubMed:3283102). Catalyzes the
CC stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-
CC diaminoheptanedioate (meso-DAP) (PubMed:6378903, PubMed:3031013,
CC PubMed:3042781). {ECO:0000269|PubMed:3031013,
CC ECO:0000269|PubMed:3042781, ECO:0000269|PubMed:3283102,
CC ECO:0000269|PubMed:6378903}.
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:0000269|PubMed:3042781,
CC ECO:0000269|PubMed:6378903};
CC -!- ACTIVITY REGULATION: Inhibited by 2-(4-amino-4-carboxybutyl)aziri-dine-
CC 2-carboxylate (aziDAP) and iodoacetamide. {ECO:0000269|PubMed:2197412,
CC ECO:0000269|PubMed:3042781, ECO:0000269|PubMed:6378903}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.16 mM for D,L-DAP (at pH 7.8 and at 25 degrees Celsius)
CC {ECO:0000269|PubMed:3042781, ECO:0000269|PubMed:6378903};
CC KM=0.26 mM for L,L-DAP (at pH 7.8 and at 25 degrees Celsius)
CC {ECO:0000269|PubMed:3042781, ECO:0000269|PubMed:6378903};
CC KM=0.36 mM for L,L-DAP (at pH 7.8 and at 25 degrees Celsius)
CC {ECO:0000269|PubMed:3042781, ECO:0000269|PubMed:6378903};
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:0000305|PubMed:3283102}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:23426375,
CC ECO:0000269|PubMed:6378903}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene show an unusual large LL-
CC diaminopimelic acid (LL-DAP) pool and an important variations of the
CC LL-DAP/meso-DAP ratio incorporated in the peptidoglycan.
CC {ECO:0000269|PubMed:3283102}.
CC -!- MISCELLANEOUS: DapF utilizes a two-base mechanism involving a pair of
CC cysteine residues (Cys-73 and Cys-217). {ECO:0000269|PubMed:6378903}.
CC -!- SIMILARITY: Belongs to the diaminopimelate epimerase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA67605.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAA31413.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; X12968; CAA31413.1; ALT_INIT; Genomic_DNA.
DR EMBL; M87049; AAA67605.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC76812.2; -; Genomic_DNA.
DR EMBL; AP009048; BAE77491.1; -; Genomic_DNA.
DR EMBL; M38257; AAA24761.1; -; Genomic_DNA.
DR EMBL; X66782; CAA47282.1; -; Genomic_DNA.
DR PIR; B65185; S01913.
DR RefSeq; NP_418254.2; NC_000913.3.
DR RefSeq; WP_001160654.1; NZ_STEB01000021.1.
DR PDB; 4IJZ; X-ray; 2.00 A; A/B=1-274.
DR PDB; 4IK0; X-ray; 2.05 A; A/B=1-274.
DR PDB; 5YGU; X-ray; 2.30 A; A=1-274.
DR PDB; 6VCK; X-ray; 2.69 A; A=1-274.
DR PDB; 6VCL; X-ray; 2.06 A; A=1-274.
DR PDB; 6VCM; X-ray; 2.35 A; A=1-274.
DR PDBsum; 4IJZ; -.
DR PDBsum; 4IK0; -.
DR PDBsum; 5YGU; -.
DR PDBsum; 6VCK; -.
DR PDBsum; 6VCL; -.
DR PDBsum; 6VCM; -.
DR AlphaFoldDB; P0A6K1; -.
DR SMR; P0A6K1; -.
DR BioGRID; 4263254; 9.
DR DIP; DIP-47856N; -.
DR IntAct; P0A6K1; 2.
DR STRING; 511145.b3809; -.
DR jPOST; P0A6K1; -.
DR PaxDb; P0A6K1; -.
DR PRIDE; P0A6K1; -.
DR EnsemblBacteria; AAC76812; AAC76812; b3809.
DR EnsemblBacteria; BAE77491; BAE77491; BAE77491.
DR GeneID; 66672284; -.
DR GeneID; 948364; -.
DR KEGG; ecj:JW5592; -.
DR KEGG; eco:b3809; -.
DR PATRIC; fig|511145.12.peg.3925; -.
DR EchoBASE; EB0205; -.
DR eggNOG; COG0253; Bacteria.
DR HOGENOM; CLU_053306_1_1_6; -.
DR InParanoid; P0A6K1; -.
DR OMA; HVAMRVH; -.
DR PhylomeDB; P0A6K1; -.
DR BioCyc; EcoCyc:DIAMINOPIMEPIM-MON; -.
DR BioCyc; MetaCyc:DIAMINOPIMEPIM-MON; -.
DR SABIO-RK; P0A6K1; -.
DR UniPathway; UPA00034; UER00025.
DR PRO; PR:P0A6K1; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0008837; F:diaminopimelate epimerase activity; IDA:EcoCyc.
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 3D-structure; Amino-acid biosynthesis; Cytoplasm; Isomerase;
KW Lysine biosynthesis; Reference proteome.
FT CHAIN 1..274
FT /note="Diaminopimelate epimerase"
FT /id="PRO_0000149838"
FT ACT_SITE 73
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT ACT_SITE 217
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 11
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 44
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 64
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 74..75
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 157
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 190
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 208..209
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 SITE 159
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 208
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 268
FT /note="Important for dimerization"
FT /evidence="ECO:0000269|PubMed:23426375"
FT MUTAGEN 268
FT /note="Y->A: Significantly less active than the wild-type
FT dimer and unable to dimerize."
FT /evidence="ECO:0000269|PubMed:23426375"
FT CONFLICT 98
FT /note="S -> T (in Ref. 1; CAA31413)"
FT /evidence="ECO:0000305"
FT CONFLICT 160..161
FT /note="CV -> WL (in Ref. 1; CAA31413)"
FT /evidence="ECO:0000305"
FT CONFLICT 200..201
FT /note="EH -> DD (in Ref. 1; CAA31413)"
FT /evidence="ECO:0000305"
FT STRAND 2..8
FT /evidence="ECO:0007829|PDB:4IJZ"
FT STRAND 11..17
FT /evidence="ECO:0007829|PDB:4IJZ"
FT STRAND 19..21
FT /evidence="ECO:0007829|PDB:4IJZ"
FT HELIX 27..34
FT /evidence="ECO:0007829|PDB:4IJZ"
FT TURN 36..38
FT /evidence="ECO:0007829|PDB:4IJZ"
FT STRAND 43..49
FT /evidence="ECO:0007829|PDB:4IJZ"
FT STRAND 57..64
FT /evidence="ECO:0007829|PDB:4IJZ"
FT STRAND 69..71
FT /evidence="ECO:0007829|PDB:4IJZ"
FT HELIX 74..86
FT /evidence="ECO:0007829|PDB:4IJZ"
FT STRAND 93..99
FT /evidence="ECO:0007829|PDB:4IJZ"
FT STRAND 102..108
FT /evidence="ECO:0007829|PDB:4IJZ"
FT STRAND 114..117
FT /evidence="ECO:0007829|PDB:4IJZ"
FT HELIX 125..127
FT /evidence="ECO:0007829|PDB:4IJZ"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:6VCK"
FT STRAND 137..143
FT /evidence="ECO:0007829|PDB:4IJZ"
FT STRAND 146..165
FT /evidence="ECO:0007829|PDB:4IJZ"
FT HELIX 167..169
FT /evidence="ECO:0007829|PDB:4IJZ"
FT HELIX 172..180
FT /evidence="ECO:0007829|PDB:4IJZ"
FT STRAND 190..198
FT /evidence="ECO:0007829|PDB:4IJZ"
FT STRAND 201..208
FT /evidence="ECO:0007829|PDB:4IJZ"
FT TURN 209..211
FT /evidence="ECO:0007829|PDB:4IJZ"
FT STRAND 212..215
FT /evidence="ECO:0007829|PDB:4IK0"
FT HELIX 218..230
FT /evidence="ECO:0007829|PDB:4IJZ"
FT STRAND 236..242
FT /evidence="ECO:0007829|PDB:4IJZ"
FT STRAND 245..251
FT /evidence="ECO:0007829|PDB:4IJZ"
FT STRAND 258..262
FT /evidence="ECO:0007829|PDB:4IJZ"
FT STRAND 265..272
FT /evidence="ECO:0007829|PDB:4IJZ"
SQ SEQUENCE 274 AA; 30209 MW; 4ACC137D2F5BD240 CRC64;
MQFSKMHGLG NDFMVVDAVT QNVFFSPELI RRLADRHLGV GFDQLLVVEP PYDPELDFHY
RIFNADGSEV AQCGNGARCF ARFVRLKGLT NKRDIRVSTA NGRMVLTVTD DDLVRVNMGE
PNFEPSAVPF RANKAEKTYI MRAAEQTILC GVVSMGNPHC VIQVDDVDTA AVETLGPVLE
SHERFPERAN IGFMQVVKRE HIRLRVYERG AGETQACGSG ACAAVAVGIQ QGLLAEEVRV
ELPGGRLDIA WKGPGHPLYM TGPAVHVYDG FIHL
