DAPF_ACIB3
ID DAPF_ACIB3 Reviewed; 281 AA.
AC B7GY71;
DT 14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT 10-FEB-2009, sequence version 1.
DT 03-AUG-2022, entry version 71.
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=ABBFA_000848;
OS Acinetobacter baumannii (strain AB307-0294).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Moraxellales; Moraxellaceae;
OC Acinetobacter; Acinetobacter calcoaceticus/baumannii complex.
OX NCBI_TaxID=557600;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AB307-0294;
RX PubMed=18931120; DOI=10.1128/jb.00834-08;
RA Adams M.D., Goglin K., Molyneaux N., Hujer K.M., Lavender H., Jamison J.J.,
RA MacDonald I.J., Martin K.M., Russo T., Campagnari A.A., Hujer A.M.,
RA Bonomo R.A., Gill S.R.;
RT "Comparative genome sequence analysis of multidrug-resistant Acinetobacter
RT baumannii.";
RL J. Bacteriol. 190:8053-8064(2008).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 1-280, AND SUBUNIT.
RA Mayclin S.J., Lorimer D.D., Edwards T.E.;
RT "Structure of a diaminopimelate epimerase from Acinetobacter baumannii.";
RL Submitted (DEC-2015) 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:0000305|Ref.2}.
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; CP001172; ACJ59349.1; -; Genomic_DNA.
DR RefSeq; WP_000923484.1; NZ_CP001172.1.
DR PDB; 5HA4; X-ray; 1.85 A; A/B=1-280.
DR PDBsum; 5HA4; -.
DR AlphaFoldDB; B7GY71; -.
DR SMR; B7GY71; -.
DR HOGENOM; CLU_053306_1_1_6; -.
DR OMA; HVAMRVH; -.
DR UniPathway; UPA00034; UER00025.
DR Proteomes; UP000006924; 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.
FT CHAIN 1..281
FT /note="Diaminopimelate epimerase"
FT /id="PRO_1000118659"
FT ACT_SITE 75
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT ACT_SITE 220
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 13
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 46
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 66
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 76..77
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 160
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 193
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 211..212
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 221..222
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT SITE 162
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 211
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 270
FT /note="Important for dimerization"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT STRAND 3..10
FT /evidence="ECO:0007829|PDB:5HA4"
FT STRAND 13..19
FT /evidence="ECO:0007829|PDB:5HA4"
FT HELIX 29..36
FT /evidence="ECO:0007829|PDB:5HA4"
FT TURN 38..40
FT /evidence="ECO:0007829|PDB:5HA4"
FT STRAND 45..51
FT /evidence="ECO:0007829|PDB:5HA4"
FT STRAND 59..66
FT /evidence="ECO:0007829|PDB:5HA4"
FT HELIX 78..88
FT /evidence="ECO:0007829|PDB:5HA4"
FT STRAND 99..101
FT /evidence="ECO:0007829|PDB:5HA4"
FT STRAND 104..106
FT /evidence="ECO:0007829|PDB:5HA4"
FT HELIX 112..114
FT /evidence="ECO:0007829|PDB:5HA4"
FT STRAND 116..119
FT /evidence="ECO:0007829|PDB:5HA4"
FT HELIX 127..129
FT /evidence="ECO:0007829|PDB:5HA4"
FT STRAND 141..144
FT /evidence="ECO:0007829|PDB:5HA4"
FT HELIX 146..148
FT /evidence="ECO:0007829|PDB:5HA4"
FT STRAND 150..166
FT /evidence="ECO:0007829|PDB:5HA4"
FT TURN 170..172
FT /evidence="ECO:0007829|PDB:5HA4"
FT HELIX 175..183
FT /evidence="ECO:0007829|PDB:5HA4"
FT STRAND 193..201
FT /evidence="ECO:0007829|PDB:5HA4"
FT STRAND 204..211
FT /evidence="ECO:0007829|PDB:5HA4"
FT TURN 212..214
FT /evidence="ECO:0007829|PDB:5HA4"
FT STRAND 215..218
FT /evidence="ECO:0007829|PDB:5HA4"
FT HELIX 221..233
FT /evidence="ECO:0007829|PDB:5HA4"
FT STRAND 239..245
FT /evidence="ECO:0007829|PDB:5HA4"
FT STRAND 248..253
FT /evidence="ECO:0007829|PDB:5HA4"
FT STRAND 261..264
FT /evidence="ECO:0007829|PDB:5HA4"
FT STRAND 267..274
FT /evidence="ECO:0007829|PDB:5HA4"
FT HELIX 276..279
FT /evidence="ECO:0007829|PDB:5HA4"
SQ SEQUENCE 281 AA; 31139 MW; 700E4DB6C3C49032 CRC64;
MLLEFTKMHG LGNDFMVVDL ISQRAYLDTA TIQRLADRHF GVGFDQLLIV EPPDVPEADF
KYRIFNADGS EVEQCGNGVR CFARFVHERH LTNKTNITVQ TKAGIVKPEL GQNGWVRVNM
GYPKFLPNEI PFVAEEPEAL YTLELANDQN ISIDVVNMGN PHAVTIVPDV LTADVAGIGP
QVESHKRFPE RVNAGFMQVI DDKHVRLRVF ERGVGETLAC GTGACAAAVS GMRRGLLANS
VEVELAGGKL QIEWQEGDVV WMTGPTTHVY DGRLDLRYFQ G
