DAPF_BACAN
ID DAPF_BACAN Reviewed; 288 AA.
AC Q81XR2; Q6F086; Q6HRI9;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, 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};
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=BA_5170, GBAA_5170, BAS4806;
OS Bacillus anthracis.
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus;
OC Bacillus cereus group.
OX NCBI_TaxID=1392;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Ames / isolate Porton;
RX PubMed=12721629; DOI=10.1038/nature01586;
RA Read T.D., Peterson S.N., Tourasse N.J., Baillie L.W., Paulsen I.T.,
RA Nelson K.E., Tettelin H., Fouts D.E., Eisen J.A., Gill S.R.,
RA Holtzapple E.K., Okstad O.A., Helgason E., Rilstone J., Wu M.,
RA Kolonay J.F., Beanan M.J., Dodson R.J., Brinkac L.M., Gwinn M.L.,
RA DeBoy R.T., Madpu R., Daugherty S.C., Durkin A.S., Haft D.H., Nelson W.C.,
RA Peterson J.D., Pop M., Khouri H.M., Radune D., Benton J.L., Mahamoud Y.,
RA Jiang L., Hance I.R., Weidman J.F., Berry K.J., Plaut R.D., Wolf A.M.,
RA Watkins K.L., Nierman W.C., Hazen A., Cline R.T., Redmond C., Thwaite J.E.,
RA White O., Salzberg S.L., Thomason B., Friedlander A.M., Koehler T.M.,
RA Hanna P.C., Kolstoe A.-B., Fraser C.M.;
RT "The genome sequence of Bacillus anthracis Ames and comparison to closely
RT related bacteria.";
RL Nature 423:81-86(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Ames ancestor;
RX PubMed=18952800; DOI=10.1128/jb.01347-08;
RA Ravel J., Jiang L., Stanley S.T., Wilson M.R., Decker R.S., Read T.D.,
RA Worsham P., Keim P.S., Salzberg S.L., Fraser-Liggett C.M., Rasko D.A.;
RT "The complete genome sequence of Bacillus anthracis Ames 'Ancestor'.";
RL J. Bacteriol. 191:445-446(2009).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Sterne;
RA Brettin T.S., Bruce D., Challacombe J.F., Gilna P., Han C., Hill K.,
RA Hitchcock P., Jackson P., Keim P., Longmire J., Lucas S., Okinaka R.,
RA Richardson P., Rubin E., Tice H.;
RT "Complete genome sequence of Bacillus anthracis Sterne.";
RL Submitted (JAN-2004) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.49 ANGSTROMS), AND SUBUNIT.
RA Matho M.H., Fukuda K., Santelli E., Jaroszewski L., Liddington R.C.,
RA Roper D.;
RT "Crystal structure of the catalytically active form of diamin epimerase
RT from Bacillus anthracis.";
RL Submitted (FEB-2007) to the PDB data bank.
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:0000269|Ref.4}.
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; AE016879; AAP28840.1; -; Genomic_DNA.
DR EMBL; AE017225; AAT57099.1; -; Genomic_DNA.
DR EMBL; AE017334; AAT70160.1; -; Genomic_DNA.
DR RefSeq; NP_847354.1; NC_003997.3.
DR RefSeq; WP_000077386.1; NZ_WXXJ01000017.1.
DR RefSeq; YP_031049.1; NC_005945.1.
DR PDB; 2OTN; X-ray; 2.40 A; A/B=1-288.
DR PDBsum; 2OTN; -.
DR AlphaFoldDB; Q81XR2; -.
DR SMR; Q81XR2; -.
DR IntAct; Q81XR2; 3.
DR STRING; 260799.BAS4806; -.
DR DNASU; 1084119; -.
DR EnsemblBacteria; AAP28840; AAP28840; BA_5170.
DR EnsemblBacteria; AAT70160; AAT70160; GBAA_5170.
DR GeneID; 45024796; -.
DR KEGG; ban:BA_5170; -.
DR KEGG; bar:GBAA_5170; -.
DR KEGG; bat:BAS4806; -.
DR PATRIC; fig|198094.11.peg.5132; -.
DR eggNOG; COG0253; Bacteria.
DR HOGENOM; CLU_053306_3_0_9; -.
DR OMA; HVAMRVH; -.
DR UniPathway; UPA00034; UER00025.
DR EvolutionaryTrace; Q81XR2; -.
DR Proteomes; UP000000427; Chromosome.
DR Proteomes; UP000000594; 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 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Cytoplasm; Isomerase;
KW Lysine biosynthesis; Reference proteome.
FT CHAIN 1..288
FT /note="Diaminopimelate epimerase"
FT /id="PRO_1000011837"
FT ACT_SITE 76
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT ACT_SITE 226
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 14
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 67
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 77..78
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 166
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 199
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 217..218
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 227..228
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT SITE 168
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 217
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 STRAND 1..11
FT /evidence="ECO:0007829|PDB:2OTN"
FT STRAND 14..20
FT /evidence="ECO:0007829|PDB:2OTN"
FT TURN 21..23
FT /evidence="ECO:0007829|PDB:2OTN"
FT HELIX 28..30
FT /evidence="ECO:0007829|PDB:2OTN"
FT HELIX 31..39
FT /evidence="ECO:0007829|PDB:2OTN"
FT TURN 41..43
FT /evidence="ECO:0007829|PDB:2OTN"
FT STRAND 48..54
FT /evidence="ECO:0007829|PDB:2OTN"
FT STRAND 57..67
FT /evidence="ECO:0007829|PDB:2OTN"
FT TURN 76..79
FT /evidence="ECO:0007829|PDB:2OTN"
FT HELIX 80..89
FT /evidence="ECO:0007829|PDB:2OTN"
FT STRAND 94..102
FT /evidence="ECO:0007829|PDB:2OTN"
FT STRAND 105..126
FT /evidence="ECO:0007829|PDB:2OTN"
FT HELIX 132..134
FT /evidence="ECO:0007829|PDB:2OTN"
FT STRAND 143..152
FT /evidence="ECO:0007829|PDB:2OTN"
FT STRAND 155..172
FT /evidence="ECO:0007829|PDB:2OTN"
FT HELIX 176..178
FT /evidence="ECO:0007829|PDB:2OTN"
FT TURN 181..183
FT /evidence="ECO:0007829|PDB:2OTN"
FT HELIX 184..189
FT /evidence="ECO:0007829|PDB:2OTN"
FT STRAND 199..207
FT /evidence="ECO:0007829|PDB:2OTN"
FT STRAND 210..216
FT /evidence="ECO:0007829|PDB:2OTN"
FT STRAND 218..220
FT /evidence="ECO:0007829|PDB:2OTN"
FT HELIX 227..239
FT /evidence="ECO:0007829|PDB:2OTN"
FT STRAND 249..252
FT /evidence="ECO:0007829|PDB:2OTN"
FT STRAND 257..262
FT /evidence="ECO:0007829|PDB:2OTN"
FT STRAND 268..273
FT /evidence="ECO:0007829|PDB:2OTN"
FT STRAND 275..286
FT /evidence="ECO:0007829|PDB:2OTN"
SQ SEQUENCE 288 AA; 31613 MW; F82364D2AC4202CA CRC64;
MSQFSFTKMH GLGNSYIYVN MFEEQIPEED LALVAEKVSN INTGIGADGM ILICPSDVAP
VKMRMFNNDG SEGKSCGNGL RCVAKYAYEH KLVEDTVFTI ETLAGIVTAE VTVEEGKVTL
AKIDMGAPRL TRAEIPMLGE GETPFIRENF LYNNHRYAFT AVSMGNPHAV IFVDDVEQAP
LTTLGPVLET HEMFPERVNV EFIEILNEEE MNFRVWERGS GVTQACGTGA CAAVVASILN
GKMERGKEIT VHLAGGDLMI AWTEEGNVLM KGPAEVICRG VYEYKIEA
