DAPF_MYCTU
ID DAPF_MYCTU Reviewed; 289 AA.
AC P9WP19; L0TC29; O33231; P63897;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 39.
DE RecName: Full=Diaminopimelate epimerase {ECO:0000303|PubMed:16907737};
DE Short=DAP epimerase {ECO:0000303|PubMed:16907737};
DE EC=5.1.1.7 {ECO:0000269|PubMed:16907737, ECO:0000269|PubMed:18269631};
DE AltName: Full=PLP-independent amino acid racemase {ECO:0000255|HAMAP-Rule:MF_00197};
GN Name=dapF {ECO:0000303|PubMed:16907737}; OrderedLocusNames=Rv2726c;
GN ORFNames=MTCY154.06c;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP IDENTIFICATION AS A DRUG TARGET [LARGE SCALE ANALYSIS].
RX PubMed=19099550; DOI=10.1186/1752-0509-2-109;
RA Raman K., Yeturu K., Chandra N.;
RT "targetTB: a target identification pipeline for Mycobacterium tuberculosis
RT through an interactome, reactome and genome-scale structural analysis.";
RL BMC Syst. Biol. 2:109-109(2008).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=16907737; DOI=10.1111/j.1574-6968.2006.00356.x;
RA Usha V., Dover L.G., Roper D.L., Lloyd A.J., Besra G.S.;
RT "Use of a codon alteration strategy in a novel approach to cloning the
RT Mycobacterium tuberculosis diaminopimelic acid epimerase.";
RL FEMS Microbiol. Lett. 262:39-47(2006).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF CYS-87 AND CYS-226,
RP BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITE, AND ACTIVITY REGULATION.
RX PubMed=18269631; DOI=10.1111/j.1574-6968.2007.01049.x;
RA Usha V., Dover L.G., Roper D.L., Besra G.S.;
RT "Characterization of Mycobacterium tuberculosis diaminopimelic acid
RT epimerase: paired cysteine residues are crucial for racemization.";
RL FEMS Microbiol. Lett. 280:57-63(2008).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS), AND ACTIVE SITE.
RX PubMed=19307721; DOI=10.1107/s0907444909002522;
RA Usha V., Dover L.G., Roper D.I., Futterer K., Besra G.S.;
RT "Structure of the diaminopimelate epimerase DapF from Mycobacterium
RT tuberculosis.";
RL Acta Crystallogr. D 65:383-387(2009).
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:0000269|PubMed:16907737, ECO:0000269|PubMed:18269631}.
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:16907737,
CC ECO:0000269|PubMed:18269631};
CC -!- ACTIVITY REGULATION: Inhibited by sulphydryl alkylating agents, 2-
CC nitro-5-thiocyanatobenzoate (NTCB), 5,50-dithiobis(2-nitrobenzoic acid)
CC (DTNB) and 1,2-benzisothiazolidine 3-one (BIT) at nanomolar
CC concentrations. {ECO:0000269|PubMed:18269631}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=165.93 uM for meso-DAP (at pH 7.5 and at 30 degrees Celsius)
CC {ECO:0000269|PubMed:18269631};
CC KM=1217 uM for meso-DAP (at pH 7.5 and at 30 degrees Celsius)
CC {ECO:0000269|PubMed:16907737};
CC Note=kcat is 0.1465 sec(-1) for epimerase activity.
CC {ECO:0000269|PubMed:18269631};
CC pH dependence:
CC Optimum pH is 7.5. {ECO:0000269|PubMed:16907737};
CC Temperature dependence:
CC DapF is almost 50% more active at 30 degrees Celsius than at 25
CC degrees Celsius. At 37 degrees Celsius the activity is slightly less
CC than at 30 degrees Celsius. {ECO:0000269|PubMed:16907737};
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 -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- MISCELLANEOUS: Was identified as a high-confidence drug target.
CC {ECO:0000269|PubMed:19099550}.
CC -!- SIMILARITY: Belongs to the diaminopimelate epimerase family.
CC {ECO:0000305}.
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DR EMBL; AL123456; CCP45524.1; -; Genomic_DNA.
DR PIR; E70505; E70505.
DR RefSeq; NP_217242.1; NC_000962.3.
DR RefSeq; WP_003413987.1; NZ_NVQJ01000017.1.
DR PDB; 3FVE; X-ray; 2.60 A; A=1-289.
DR PDBsum; 3FVE; -.
DR AlphaFoldDB; P9WP19; -.
DR SMR; P9WP19; -.
DR STRING; 83332.Rv2726c; -.
DR PaxDb; P9WP19; -.
DR DNASU; 888614; -.
DR GeneID; 45426713; -.
DR GeneID; 888614; -.
DR KEGG; mtu:Rv2726c; -.
DR TubercuList; Rv2726c; -.
DR eggNOG; COG0253; Bacteria.
DR OMA; HVAMRVH; -.
DR PhylomeDB; P9WP19; -.
DR BRENDA; 5.1.1.7; 3445.
DR UniPathway; UPA00034; UER00025.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
DR GO; GO:0008837; F:diaminopimelate epimerase activity; IDA:MTBBASE.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IDA:MTBBASE.
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..289
FT /note="Diaminopimelate epimerase"
FT /id="PRO_0000149853"
FT ACT_SITE 87
FT /note="Proton donor"
FT /evidence="ECO:0000269|PubMed:18269631,
FT ECO:0000305|PubMed:19307721"
FT ACT_SITE 226
FT /note="Proton acceptor"
FT /evidence="ECO:0000269|PubMed:18269631,
FT ECO:0000305|PubMed:19307721"
FT BINDING 11
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 78
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 88..89
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 163
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 165
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 MUTAGEN 87
FT /note="C->A: Completely abolishes the diaminopimelate
FT epimerase activity."
FT /evidence="ECO:0000269|PubMed:18269631"
FT MUTAGEN 87
FT /note="C->S: Strongly reduces the diaminopimelate epimerase
FT activity."
FT /evidence="ECO:0000269|PubMed:18269631"
FT MUTAGEN 226
FT /note="C->A: Completely abolishes the diaminopimelate
FT epimerase activity."
FT /evidence="ECO:0000269|PubMed:18269631"
FT MUTAGEN 226
FT /note="C->S: Strongly reduces the diaminopimelate epimerase
FT activity."
FT /evidence="ECO:0000269|PubMed:18269631"
FT STRAND 1..10
FT /evidence="ECO:0007829|PDB:3FVE"
FT STRAND 12..17
FT /evidence="ECO:0007829|PDB:3FVE"
FT HELIX 27..34
FT /evidence="ECO:0007829|PDB:3FVE"
FT TURN 36..38
FT /evidence="ECO:0007829|PDB:3FVE"
FT STRAND 43..50
FT /evidence="ECO:0007829|PDB:3FVE"
FT HELIX 51..56
FT /evidence="ECO:0007829|PDB:3FVE"
FT STRAND 71..78
FT /evidence="ECO:0007829|PDB:3FVE"
FT HELIX 91..100
FT /evidence="ECO:0007829|PDB:3FVE"
FT STRAND 107..112
FT /evidence="ECO:0007829|PDB:3FVE"
FT STRAND 118..125
FT /evidence="ECO:0007829|PDB:3FVE"
FT STRAND 127..135
FT /evidence="ECO:0007829|PDB:3FVE"
FT STRAND 140..147
FT /evidence="ECO:0007829|PDB:3FVE"
FT STRAND 155..170
FT /evidence="ECO:0007829|PDB:3FVE"
FT TURN 175..178
FT /evidence="ECO:0007829|PDB:3FVE"
FT TURN 191..193
FT /evidence="ECO:0007829|PDB:3FVE"
FT STRAND 199..204
FT /evidence="ECO:0007829|PDB:3FVE"
FT STRAND 210..217
FT /evidence="ECO:0007829|PDB:3FVE"
FT TURN 218..220
FT /evidence="ECO:0007829|PDB:3FVE"
FT HELIX 227..240
FT /evidence="ECO:0007829|PDB:3FVE"
FT STRAND 244..252
FT /evidence="ECO:0007829|PDB:3FVE"
FT STRAND 255..261
FT /evidence="ECO:0007829|PDB:3FVE"
FT STRAND 266..280
FT /evidence="ECO:0007829|PDB:3FVE"
FT HELIX 282..286
FT /evidence="ECO:0007829|PDB:3FVE"
SQ SEQUENCE 289 AA; 29698 MW; 197FE4B43CD8A022 CRC64;
MIFAKGHGTQ NDFVLLPDVD AELVLTAARV AALCDRRKGL GADGVLRVTT AGAAQAVGVL
DSLPEGVRVT DWYMDYRNAD GSAAQMCGNG VRVFAHYLRA SGLEVRDEFV VGSLAGPRPV
TCHHVEAAYA DVSVDMGKAN RLGAGEAVVG GRRFHGLAVD VGNPHLACVD SQLTVDGLAA
LDVGAPVSFD GAQFPDGVNV EVLTAPVDGA VWMRVHERGV GETRSCGTGT VAAAVAALAA
VGSPTGTLTV HVPGGEVVVT VTDATSFLRG PSVLVARGDL ADDWWNAMG
