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Diaminopimelate epimerase (DAP epimerase) (EC 5.1.1.7) (PLP-independent amino acid racemase)

 DAPF_HAEIN              Reviewed;         274 AA.
P44859;
01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
01-NOV-1995, sequence version 1.
12-SEP-2018, entry version 121.
RecName: Full=Diaminopimelate epimerase {ECO:0000303|PubMed:10194362};
Short=DAP epimerase {ECO:0000303|PubMed:10194362};
EC=5.1.1.7 {ECO:0000269|PubMed:10194362};
AltName: Full=PLP-independent amino acid racemase {ECO:0000303|PubMed:10194362};
Name=dapF {ECO:0000303|PubMed:10194362}; OrderedLocusNames=HI_0750;
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd).
Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales;
Pasteurellaceae; Haemophilus.
NCBI_TaxID=71421;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 51907 / DSM 11121 / KW20 / Rd;
PubMed=7542800; DOI=10.1126/science.7542800;
Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F.,
Kerlavage A.R., Bult C.J., Tomb J.-F., Dougherty B.A., Merrick J.M.,
McKenney K., Sutton G.G., FitzHugh W., Fields C.A., Gocayne J.D.,
Scott J.D., Shirley R., Liu L.-I., Glodek A., Kelley J.M.,
Weidman J.F., Phillips C.A., Spriggs T., Hedblom E., Cotton M.D.,
Utterback T.R., Hanna M.C., Nguyen D.T., Saudek D.M., Brandon R.C.,
Fine L.D., Fritchman J.L., Fuhrmann J.L., Geoghagen N.S.M.,
Gnehm C.L., McDonald L.A., Small K.V., Fraser C.M., Smith H.O.,
Venter J.C.;
"Whole-genome random sequencing and assembly of Haemophilus influenzae
Rd.";
Science 269:496-512(1995).
[2]
FUNCTION, CATALYTIC ACTIVITY, REACTION MECHANISM, AND
BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=10194362; DOI=10.1021/bi982911f;
Koo C.W., Blanchard J.S.;
"Chemical mechanism of Haemophilus influenzae diaminopimelate
epimerase.";
Biochemistry 38:4416-4422(1999).
[3]
MUTAGENESIS OF CYS-73 AND CYS-217, ACTIVE SITE, AND ACTIVITY
REGULATION.
DOI=10.1021/ja001193t;
Koo C.W., Sutherland A., Vederas J.C., Blanchard J.S.;
"Identification of active site cysteine residues that function as
general bases: diaminopimelate epimerase.";
J. Am. Chem. Soc. 122:6122-6123(2000).
[4]
X-RAY CRYSTALLOGRAPHY (2.72 ANGSTROMS), ACTIVE SITE, AND SUBUNIT.
PubMed=9843410; DOI=10.1021/bi982138o;
Cirilli M., Zheng R., Scapin G., Blanchard J.S.;
"Structural symmetry: the three-dimensional structure of Haemophilus
influenzae diaminopimelate epimerase.";
Biochemistry 37:16452-16458(1998).
[5]
X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS), AND REACTION MECHANISM.
PubMed=14747737; DOI=10.1107/S0907444903027999;
Lloyd A.J., Huyton T., Turkenburg J., Roper D.I.;
"Refinement of Haemophilus influenzae diaminopimelic acid epimerase
(DapF) at 1.75 A resolution suggests a mechanism for stereocontrol
during catalysis.";
Acta Crystallogr. D 60:397-400(2004).
[6]
X-RAY CRYSTALLOGRAPHY (1.35 ANGSTROMS) IN COMPLEX WITH SUBSTRATE
ANALOGS, FUNCTION, SUBSTRATE SPECIFICITY, ACTIVITY REGULATION, ACTIVE
SITE, AND REACTION MECHANISM.
PubMed=16723397; DOI=10.1073/pnas.0602537103;
Pillai B., Cherney M.M., Diaper C.M., Sutherland A., Blanchard J.S.,
Vederas J.C., James M.N.;
"Structural insights into stereochemical inversion by diaminopimelate
epimerase: an antibacterial drug target.";
Proc. Natl. Acad. Sci. U.S.A. 103:8668-8673(2006).
[7]
X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) OF MUTANT SER-73 AND SER-217,
MUTAGENESIS OF CYS-73 AND CYS-217, AND SUBUNIT.
PubMed=17889830; DOI=10.1016/j.bbrc.2007.09.012;
Pillai B., Cherney M., Diaper C.M., Sutherland A., Blanchard J.S.,
Vederas J.C., James M.N.;
"Dynamics of catalysis revealed from the crystal structures of mutants
of diaminopimelate epimerase.";
Biochem. Biophys. Res. Commun. 363:547-553(2007).
-!- FUNCTION: Catalyzes the stereoinversion of LL-2,6-
diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-
DAP), a precursor of L-lysine and an essential component of the
bacterial peptidoglycan (PubMed:10194362, PubMed:16723397). Only
accepts DAP isomers with the L configuration (PubMed:16723397).
{ECO:0000269|PubMed:10194362, ECO:0000269|PubMed:16723397}.
-!- CATALYTIC ACTIVITY: LL-2,6-diaminoheptanedioate = meso-
diaminoheptanedioate. {ECO:0000269|PubMed:10194362}.
-!- ACTIVITY REGULATION: Inhibited by LL-aziridino (LL-AziDAP), DL-
aziridino (DL-AziDAP) (PubMed:16723397). Also inhibited by
(2S,3R,6S)-2,6-diamino-3-fluoropimelate (L,L-3-fluoro-DAP) and
(2R,3S,6S)-2,6-diamino-3-fluoropimelate (D,L-3-fluoro-DAP)
(Ref.3). {ECO:0000269|PubMed:16723397, ECO:0000269|Ref.3}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.7 mM for L,L-DAP (at pH 7.8) {ECO:0000269|PubMed:10194362};
KM=1.1 mM for D,L-DAP (at pH 7.8) {ECO:0000269|PubMed:10194362};
Note=Kcat is 128 and 82 sec(-1) for L,L-DAP and D,L-DAP,
respectively. {ECO:0000269|PubMed:10194362};
-!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
pathway; DL-2,6-diaminopimelate from LL-2,6-diaminopimelate: step
1/1. {ECO:0000305}.
-!- SUBUNIT: Homodimer (Potential). Previously DapF has been proposed
to be a monomer, however it seems that it adopts a dimeric
structure (PubMed:9843410, PubMed:17889830). {ECO:0000255|HAMAP-
Rule:MF_00197, ECO:0000269|PubMed:17889830,
ECO:0000269|PubMed:9843410}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
-!- MISCELLANEOUS: DapF utilizes a two-base mechanism involving a pair
of cysteine residues (Cys-73 and Cys-217).
{ECO:0000269|PubMed:16723397}.
-!- SIMILARITY: Belongs to the diaminopimelate epimerase family.
{ECO:0000305}.
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EMBL; L42023; AAC22409.1; -; Genomic_DNA.
PIR; F64090; F64090.
RefSeq; NP_438909.1; NC_000907.1.
RefSeq; WP_005655521.1; NC_000907.1.
PDB; 1BWZ; X-ray; 2.72 A; A=1-274.
PDB; 1GQZ; X-ray; 1.75 A; A=1-274.
PDB; 2GKE; X-ray; 1.35 A; A=1-274.
PDB; 2GKJ; X-ray; 1.70 A; A=1-274.
PDB; 2Q9H; X-ray; 2.30 A; A=1-274.
PDB; 2Q9J; X-ray; 2.20 A; A=1-274.
PDBsum; 1BWZ; -.
PDBsum; 1GQZ; -.
PDBsum; 2GKE; -.
PDBsum; 2GKJ; -.
PDBsum; 2Q9H; -.
PDBsum; 2Q9J; -.
ProteinModelPortal; P44859; -.
SMR; P44859; -.
STRING; 71421.HI0750; -.
EnsemblBacteria; AAC22409; AAC22409; HI_0750.
GeneID; 949560; -.
KEGG; hin:HI0750; -.
PATRIC; fig|71421.8.peg.787; -.
eggNOG; ENOG4105E4Z; Bacteria.
eggNOG; COG0253; LUCA.
KO; K01778; -.
OMA; SMCGNGG; -.
PhylomeDB; P44859; -.
BioCyc; HINF71421:G1GJ1-788-MONOMER; -.
BRENDA; 5.1.1.7; 2529.
UniPathway; UPA00034; UER00025.
EvolutionaryTrace; P44859; -.
Proteomes; UP000000579; Chromosome.
GO; GO:0005829; C:cytosol; IBA:GO_Central.
GO; GO:0008837; F:diaminopimelate epimerase activity; IBA:GO_Central.
GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IBA:GO_Central.
HAMAP; MF_00197; DAP_epimerase; 1.
InterPro; IPR018510; DAP_epimerase_AS.
InterPro; IPR001653; DAP_epimerase_DapF.
PANTHER; PTHR31689; PTHR31689; 1.
Pfam; PF01678; DAP_epimerase; 2.
TIGRFAMs; TIGR00652; DapF; 1.
PROSITE; PS01326; DAP_EPIMERASE; 1.
1: Evidence at protein level;
3D-structure; Amino-acid biosynthesis; Complete proteome; Cytoplasm;
Isomerase; Lysine biosynthesis; Reference proteome.
CHAIN 1 274 Diaminopimelate epimerase.
/FTId=PRO_0000149842.
REGION 74 75 Substrate binding. {ECO:0000244|PDB:2GKE,
ECO:0000244|PDB:2GKJ,
ECO:0000269|PubMed:16723397}.
REGION 208 209 Substrate binding. {ECO:0000244|PDB:2GKE,
ECO:0000244|PDB:2GKJ,
ECO:0000269|PubMed:16723397}.
REGION 218 219 Substrate binding. {ECO:0000244|PDB:2GKE,
ECO:0000244|PDB:2GKJ,
ECO:0000269|PubMed:16723397}.
ACT_SITE 73 73 Proton donor. {ECO:0000244|PDB:1BWZ,
ECO:0000244|PDB:2GKE,
ECO:0000244|PDB:2GKJ,
ECO:0000305|PubMed:16723397,
ECO:0000305|PubMed:9843410,
ECO:0000305|Ref.3}.
ACT_SITE 217 217 Proton acceptor. {ECO:0000244|PDB:1BWZ,
ECO:0000244|PDB:2GKE,
ECO:0000244|PDB:2GKJ,
ECO:0000305|PubMed:16723397,
ECO:0000305|PubMed:9843410,
ECO:0000305|Ref.3}.
BINDING 11 11 Substrate. {ECO:0000244|PDB:2GKE,
ECO:0000244|PDB:2GKJ,
ECO:0000269|PubMed:16723397}.
BINDING 44 44 Substrate. {ECO:0000244|PDB:2GKJ,
ECO:0000269|PubMed:16723397}.
BINDING 64 64 Substrate. {ECO:0000244|PDB:2GKE,
ECO:0000244|PDB:2GKJ,
ECO:0000269|PubMed:16723397}.
BINDING 157 157 Substrate. {ECO:0000244|PDB:2GKE,
ECO:0000244|PDB:2GKJ,
ECO:0000269|PubMed:16723397}.
BINDING 190 190 Substrate. {ECO:0000244|PDB:2GKE,
ECO:0000244|PDB:2GKJ,
ECO:0000269|PubMed:16723397}.
SITE 159 159 Could be important to modulate the pK
values of the two catalytic cysteine
residues. {ECO:0000244|PDB:1BWZ,
ECO:0000305|PubMed:9843410}.
SITE 208 208 Could be important to modulate the pK
values of the two catalytic cysteine
residues. {ECO:0000244|PDB:1BWZ,
ECO:0000305|PubMed:9843410}.
SITE 268 268 Important for dimerization.
{ECO:0000250|UniProtKB:P0A6K1}.
MUTAGEN 73 73 C->A: Inactive as epimerase, but it is
able to rapidly catalyze the HF
elimination via abstraction of the C-2
hydrogen of the D,L-3-fluoro-DAP analog
and is essentially unable to catalyze the
same elimination with the L,L-3-fluoro-
DAP analog. {ECO:0000269|Ref.3}.
MUTAGEN 73 73 C->S: Enzymatically active, but it adopts
a more open conformation. It is able to
catalyze both epimerization of DAP and HF
elimination of L,L-3-fluoro-DAP and D,L-
3-fluoro-DAP. Able to slowly eliminate HF
but does not catalyze epimerization; when
associated with S-217.
{ECO:0000269|PubMed:17889830,
ECO:0000269|Ref.3}.
MUTAGEN 217 217 C->A: Inactive as epimerase. It is able
to rapidly catalyze the HF elimination
via abstraction of the C-2 hydrogen of
the L,L-3-fluoro-DAP analog and is
essentially unable to catalyze the same
elimination with the D,L-3-fluoro-DAP
analog. {ECO:0000269|Ref.3}.
MUTAGEN 217 217 C->S: Enzymatically active, but it adopts
a more open conformation. It is able to
catalyze both epimerization of DAP and HF
elimination of L,L-3-fluoro-DAP and D,L-
3-fluoro-DAP. Able to slowly eliminate HF
but does not catalyze epimerization; when
associated with S-73.
{ECO:0000269|PubMed:17889830,
ECO:0000269|Ref.3}.
STRAND 2 8 {ECO:0000244|PDB:2GKE}.
STRAND 11 17 {ECO:0000244|PDB:2GKE}.
STRAND 19 21 {ECO:0000244|PDB:2GKE}.
HELIX 27 34 {ECO:0000244|PDB:2GKE}.
TURN 36 38 {ECO:0000244|PDB:2GKE}.
STRAND 43 49 {ECO:0000244|PDB:2GKE}.
STRAND 56 64 {ECO:0000244|PDB:2GKE}.
STRAND 69 71 {ECO:0000244|PDB:2GKE}.
HELIX 74 86 {ECO:0000244|PDB:2GKE}.
STRAND 93 98 {ECO:0000244|PDB:2GKE}.
STRAND 103 108 {ECO:0000244|PDB:2GKE}.
STRAND 114 117 {ECO:0000244|PDB:2GKE}.
HELIX 125 127 {ECO:0000244|PDB:2GKE}.
STRAND 137 142 {ECO:0000244|PDB:2GKE}.
STRAND 147 163 {ECO:0000244|PDB:2GKE}.
TURN 167 169 {ECO:0000244|PDB:2GKE}.
HELIX 172 180 {ECO:0000244|PDB:2GKE}.
STRAND 190 198 {ECO:0000244|PDB:2GKE}.
STRAND 201 208 {ECO:0000244|PDB:2GKE}.
TURN 209 211 {ECO:0000244|PDB:2GKE}.
HELIX 218 230 {ECO:0000244|PDB:2GKE}.
STRAND 236 242 {ECO:0000244|PDB:2GKE}.
STRAND 245 251 {ECO:0000244|PDB:2GKE}.
STRAND 258 262 {ECO:0000244|PDB:2GKE}.
STRAND 265 271 {ECO:0000244|PDB:2GKE}.
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


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