DAPF_HAEIN
ID DAPF_HAEIN Reviewed; 274 AA.
AC P44859;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 1.
DT 03-AUG-2022, entry version 138.
DE RecName: Full=Diaminopimelate epimerase {ECO:0000303|PubMed:10194362};
DE Short=DAP epimerase {ECO:0000303|PubMed:10194362};
DE EC=5.1.1.7 {ECO:0000269|PubMed:10194362};
DE AltName: Full=PLP-independent amino acid racemase {ECO:0000303|PubMed:10194362};
GN Name=dapF {ECO:0000303|PubMed:10194362}; OrderedLocusNames=HI_0750;
OS Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales;
OC Pasteurellaceae; Haemophilus.
OX NCBI_TaxID=71421;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 51907 / DSM 11121 / KW20 / Rd;
RX PubMed=7542800; DOI=10.1126/science.7542800;
RA Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F.,
RA Kerlavage A.R., Bult C.J., Tomb J.-F., Dougherty B.A., Merrick J.M.,
RA McKenney K., Sutton G.G., FitzHugh W., Fields C.A., Gocayne J.D.,
RA Scott J.D., Shirley R., Liu L.-I., Glodek A., Kelley J.M., Weidman J.F.,
RA Phillips C.A., Spriggs T., Hedblom E., Cotton M.D., Utterback T.R.,
RA Hanna M.C., Nguyen D.T., Saudek D.M., Brandon R.C., Fine L.D.,
RA Fritchman J.L., Fuhrmann J.L., Geoghagen N.S.M., Gnehm C.L., McDonald L.A.,
RA Small K.V., Fraser C.M., Smith H.O., Venter J.C.;
RT "Whole-genome random sequencing and assembly of Haemophilus influenzae
RT Rd.";
RL Science 269:496-512(1995).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, REACTION MECHANISM, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=10194362; DOI=10.1021/bi982911f;
RA Koo C.W., Blanchard J.S.;
RT "Chemical mechanism of Haemophilus influenzae diaminopimelate epimerase.";
RL Biochemistry 38:4416-4422(1999).
RN [3]
RP MUTAGENESIS OF CYS-73 AND CYS-217, ACTIVE SITE, AND ACTIVITY REGULATION.
RX DOI=10.1021/ja001193t;
RA Koo C.W., Sutherland A., Vederas J.C., Blanchard J.S.;
RT "Identification of active site cysteine residues that function as general
RT bases: diaminopimelate epimerase.";
RL J. Am. Chem. Soc. 122:6122-6123(2000).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.72 ANGSTROMS), ACTIVE SITE, AND SUBUNIT.
RX PubMed=9843410; DOI=10.1021/bi982138o;
RA Cirilli M., Zheng R., Scapin G., Blanchard J.S.;
RT "Structural symmetry: the three-dimensional structure of Haemophilus
RT influenzae diaminopimelate epimerase.";
RL Biochemistry 37:16452-16458(1998).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS), AND REACTION MECHANISM.
RX PubMed=14747737; DOI=10.1107/s0907444903027999;
RA Lloyd A.J., Huyton T., Turkenburg J., Roper D.I.;
RT "Refinement of Haemophilus influenzae diaminopimelic acid epimerase (DapF)
RT at 1.75 A resolution suggests a mechanism for stereocontrol during
RT catalysis.";
RL Acta Crystallogr. D 60:397-400(2004).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.35 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS,
RP FUNCTION, SUBSTRATE SPECIFICITY, ACTIVITY REGULATION, ACTIVE SITE, AND
RP REACTION MECHANISM.
RX PubMed=16723397; DOI=10.1073/pnas.0602537103;
RA Pillai B., Cherney M.M., Diaper C.M., Sutherland A., Blanchard J.S.,
RA Vederas J.C., James M.N.;
RT "Structural insights into stereochemical inversion by diaminopimelate
RT epimerase: an antibacterial drug target.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:8668-8673(2006).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF MUTANT SER-73 AND SER-217,
RP MUTAGENESIS OF CYS-73 AND CYS-217, AND SUBUNIT.
RX PubMed=17889830; DOI=10.1016/j.bbrc.2007.09.012;
RA Pillai B., Cherney M., Diaper C.M., Sutherland A., Blanchard J.S.,
RA Vederas J.C., James M.N.;
RT "Dynamics of catalysis revealed from the crystal structures of mutants of
RT diaminopimelate epimerase.";
RL Biochem. Biophys. Res. Commun. 363:547-553(2007).
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:10194362, PubMed:16723397). Only accepts DAP isomers with the L
CC configuration (PubMed:16723397). {ECO:0000269|PubMed:10194362,
CC ECO:0000269|PubMed:16723397}.
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:0000269|PubMed:10194362};
CC -!- ACTIVITY REGULATION: Inhibited by LL-aziridino (LL-AziDAP), DL-
CC aziridino (DL-AziDAP) (PubMed:16723397). Also inhibited by (2S,3R,6S)-
CC 2,6-diamino-3-fluoropimelate (L,L-3-fluoro-DAP) and (2R,3S,6S)-2,6-
CC diamino-3-fluoropimelate (D,L-3-fluoro-DAP) (Ref.3).
CC {ECO:0000269|PubMed:16723397, ECO:0000269|Ref.3}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.7 mM for L,L-DAP (at pH 7.8) {ECO:0000269|PubMed:10194362};
CC KM=1.1 mM for D,L-DAP (at pH 7.8) {ECO:0000269|PubMed:10194362};
CC Note=kcat is 128 and 82 sec(-1) for L,L-DAP and D,L-DAP,
CC respectively. {ECO:0000269|PubMed:10194362};
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}.
CC -!- SUBUNIT: Homodimer (Potential). Previously DapF has been proposed to be
CC a monomer, however it seems that it adopts a dimeric structure
CC (PubMed:9843410, PubMed:17889830). {ECO:0000255|HAMAP-Rule:MF_00197,
CC ECO:0000269|PubMed:17889830, ECO:0000269|PubMed:9843410}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- MISCELLANEOUS: DapF utilizes a two-base mechanism involving a pair of
CC cysteine residues (Cys-73 and Cys-217). {ECO:0000269|PubMed:16723397}.
CC -!- SIMILARITY: Belongs to the diaminopimelate epimerase family.
CC {ECO:0000305}.
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DR EMBL; L42023; AAC22409.1; -; Genomic_DNA.
DR PIR; F64090; F64090.
DR RefSeq; NP_438909.1; NC_000907.1.
DR RefSeq; WP_005655521.1; NC_000907.1.
DR PDB; 1BWZ; X-ray; 2.72 A; A=1-274.
DR PDB; 1GQZ; X-ray; 1.75 A; A=1-274.
DR PDB; 2GKE; X-ray; 1.35 A; A=1-274.
DR PDB; 2GKJ; X-ray; 1.70 A; A=1-274.
DR PDB; 2Q9H; X-ray; 2.30 A; A=1-274.
DR PDB; 2Q9J; X-ray; 2.20 A; A=1-274.
DR PDBsum; 1BWZ; -.
DR PDBsum; 1GQZ; -.
DR PDBsum; 2GKE; -.
DR PDBsum; 2GKJ; -.
DR PDBsum; 2Q9H; -.
DR PDBsum; 2Q9J; -.
DR AlphaFoldDB; P44859; -.
DR SMR; P44859; -.
DR STRING; 71421.HI_0750; -.
DR EnsemblBacteria; AAC22409; AAC22409; HI_0750.
DR KEGG; hin:HI_0750; -.
DR PATRIC; fig|71421.8.peg.787; -.
DR eggNOG; COG0253; Bacteria.
DR HOGENOM; CLU_053306_1_1_6; -.
DR OMA; HVAMRVH; -.
DR PhylomeDB; P44859; -.
DR BioCyc; HINF71421:G1GJ1-788-MON; -.
DR BRENDA; 5.1.1.7; 2529.
DR UniPathway; UPA00034; UER00025.
DR EvolutionaryTrace; P44859; -.
DR Proteomes; UP000000579; 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 3D-structure; Amino-acid biosynthesis; Cytoplasm; Isomerase;
KW Lysine biosynthesis; Reference proteome.
FT CHAIN 1..274
FT /note="Diaminopimelate epimerase"
FT /id="PRO_0000149842"
FT ACT_SITE 73
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:16723397,
FT ECO:0000305|PubMed:9843410, ECO:0000305|Ref.3,
FT ECO:0007744|PDB:1BWZ, ECO:0007744|PDB:2GKE,
FT ECO:0007744|PDB:2GKJ"
FT ACT_SITE 217
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:16723397,
FT ECO:0000305|PubMed:9843410, ECO:0000305|Ref.3,
FT ECO:0007744|PDB:1BWZ, ECO:0007744|PDB:2GKE,
FT ECO:0007744|PDB:2GKJ"
FT BINDING 11
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16723397,
FT ECO:0007744|PDB:2GKE, ECO:0007744|PDB:2GKJ"
FT BINDING 44
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16723397,
FT ECO:0007744|PDB:2GKJ"
FT BINDING 64
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16723397,
FT ECO:0007744|PDB:2GKE, ECO:0007744|PDB:2GKJ"
FT BINDING 74..75
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16723397,
FT ECO:0007744|PDB:2GKE, ECO:0007744|PDB:2GKJ"
FT BINDING 157
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16723397,
FT ECO:0007744|PDB:2GKE, ECO:0007744|PDB:2GKJ"
FT BINDING 190
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16723397,
FT ECO:0007744|PDB:2GKE, ECO:0007744|PDB:2GKJ"
FT BINDING 208..209
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16723397,
FT ECO:0007744|PDB:2GKE, ECO:0007744|PDB:2GKJ"
FT BINDING 218..219
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16723397,
FT ECO:0007744|PDB:2GKE, ECO:0007744|PDB:2GKJ"
FT SITE 159
FT /note="Could be important to modulate the pK values of the
FT two catalytic cysteine residues"
FT /evidence="ECO:0000305|PubMed:9843410,
FT ECO:0007744|PDB:1BWZ"
FT SITE 208
FT /note="Could be important to modulate the pK values of the
FT two catalytic cysteine residues"
FT /evidence="ECO:0000305|PubMed:9843410,
FT ECO:0007744|PDB:1BWZ"
FT SITE 268
FT /note="Important for dimerization"
FT /evidence="ECO:0000250|UniProtKB:P0A6K1"
FT MUTAGEN 73
FT /note="C->A: Inactive as epimerase, but it is able to
FT rapidly catalyze the HF elimination via abstraction of the
FT C-2 hydrogen of the D,L-3-fluoro-DAP analog and is
FT essentially unable to catalyze the same elimination with
FT the L,L-3-fluoro-DAP analog."
FT /evidence="ECO:0000269|Ref.3"
FT MUTAGEN 73
FT /note="C->S: Enzymatically active, but it adopts a more
FT open conformation. It is able to catalyze both
FT epimerization of DAP and HF elimination of L,L-3-fluoro-DAP
FT and D,L-3-fluoro-DAP. Able to slowly eliminate HF but does
FT not catalyze epimerization; when associated with S-217."
FT /evidence="ECO:0000269|PubMed:17889830, ECO:0000269|Ref.3"
FT MUTAGEN 217
FT /note="C->A: Inactive as epimerase. It is able to rapidly
FT catalyze the HF elimination via abstraction of the C-2
FT hydrogen of the L,L-3-fluoro-DAP analog and is essentially
FT unable to catalyze the same elimination with the D,L-3-
FT fluoro-DAP analog."
FT /evidence="ECO:0000269|Ref.3"
FT MUTAGEN 217
FT /note="C->S: Enzymatically active, but it adopts a more
FT open conformation. It is able to catalyze both
FT epimerization of DAP and HF elimination of L,L-3-fluoro-DAP
FT and D,L-3-fluoro-DAP. Able to slowly eliminate HF but does
FT not catalyze epimerization; when associated with S-73."
FT /evidence="ECO:0000269|PubMed:17889830, ECO:0000269|Ref.3"
FT STRAND 2..8
FT /evidence="ECO:0007829|PDB:2GKE"
FT STRAND 11..17
FT /evidence="ECO:0007829|PDB:2GKE"
FT STRAND 19..21
FT /evidence="ECO:0007829|PDB:2GKE"
FT HELIX 27..34
FT /evidence="ECO:0007829|PDB:2GKE"
FT TURN 36..38
FT /evidence="ECO:0007829|PDB:2GKE"
FT STRAND 43..49
FT /evidence="ECO:0007829|PDB:2GKE"
FT STRAND 56..64
FT /evidence="ECO:0007829|PDB:2GKE"
FT STRAND 69..71
FT /evidence="ECO:0007829|PDB:2GKE"
FT HELIX 74..86
FT /evidence="ECO:0007829|PDB:2GKE"
FT STRAND 93..98
FT /evidence="ECO:0007829|PDB:2GKE"
FT STRAND 103..108
FT /evidence="ECO:0007829|PDB:2GKE"
FT STRAND 114..117
FT /evidence="ECO:0007829|PDB:2GKE"
FT HELIX 125..127
FT /evidence="ECO:0007829|PDB:2GKE"
FT STRAND 137..142
FT /evidence="ECO:0007829|PDB:2GKE"
FT STRAND 147..163
FT /evidence="ECO:0007829|PDB:2GKE"
FT TURN 167..169
FT /evidence="ECO:0007829|PDB:2GKE"
FT HELIX 172..180
FT /evidence="ECO:0007829|PDB:2GKE"
FT STRAND 190..198
FT /evidence="ECO:0007829|PDB:2GKE"
FT STRAND 201..208
FT /evidence="ECO:0007829|PDB:2GKE"
FT TURN 209..211
FT /evidence="ECO:0007829|PDB:2GKE"
FT HELIX 218..230
FT /evidence="ECO:0007829|PDB:2GKE"
FT STRAND 236..242
FT /evidence="ECO:0007829|PDB:2GKE"
FT STRAND 245..251
FT /evidence="ECO:0007829|PDB:2GKE"
FT STRAND 258..262
FT /evidence="ECO:0007829|PDB:2GKE"
FT STRAND 265..271
FT /evidence="ECO:0007829|PDB:2GKE"
SQ SEQUENCE 274 AA; 30249 MW; 321B3CDAFFE81EDA CRC64;
MQFSKMHGLG NDFVVVDGVT QNVFFTPETI RRLANRHCGI GFDQLLIVEA PYDPELDFHY
RIFNADGSEV SQCGNGARCF ARFVTLKGLT NKKDISVSTQ KGNMVLTVKD DNQIRVNMGE
PIWEPAKIPF TANKFEKNYI LRTDIQTVLC GAVSMGNPHC VVQVDDIQTA NVEQLGPLLE
SHERFPERVN AGFMQIINKE HIKLRVYERG AGETQACGSG ACAAVAVGIM QGLLNNNVQV
DLPGGSLMIE WNGVGHPLYM TGEATHIYDG FITL
