DAPF_CORGL
ID DAPF_CORGL Reviewed; 277 AA.
AC Q8NP73;
DT 25-OCT-2002, integrated into UniProtKB/Swiss-Prot.
DT 25-OCT-2002, sequence version 1.
DT 03-AUG-2022, entry version 108.
DE RecName: Full=Diaminopimelate epimerase {ECO:0000303|PubMed:12948639};
DE Short=DAP epimerase {ECO:0000303|PubMed:12948639};
DE EC=5.1.1.7 {ECO:0000269|PubMed:12948639};
DE AltName: Full=PLP-independent amino acid racemase {ECO:0000303|PubMed:12948639};
GN Name=dapF {ECO:0000303|PubMed:12948639}; OrderedLocusNames=Cgl1943, cg2129;
OS Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 /
OS JCM 1318 / LMG 3730 / NCIMB 10025).
OC Bacteria; Actinobacteria; Corynebacteriales; Corynebacteriaceae;
OC Corynebacterium.
OX NCBI_TaxID=196627;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=12743753; DOI=10.1007/s00253-003-1328-1;
RA Ikeda M., Nakagawa S.;
RT "The Corynebacterium glutamicum genome: features and impacts on
RT biotechnological processes.";
RL Appl. Microbiol. Biotechnol. 62:99-109(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=12948626; DOI=10.1016/s0168-1656(03)00154-8;
RA Kalinowski J., Bathe B., Bartels D., Bischoff N., Bott M., Burkovski A.,
RA Dusch N., Eggeling L., Eikmanns B.J., Gaigalat L., Goesmann A.,
RA Hartmann M., Huthmacher K., Kraemer R., Linke B., McHardy A.C., Meyer F.,
RA Moeckel B., Pfefferle W., Puehler A., Rey D.A., Rueckert C., Rupp O.,
RA Sahm H., Wendisch V.F., Wiegraebe I., Tauch A.;
RT "The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its
RT impact on the production of L-aspartate-derived amino acids and vitamins.";
RL J. Biotechnol. 104:5-25(2003).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, AND PATHWAY.
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=12948639; DOI=10.1016/s0168-1656(03)00156-1;
RA Hartmann M., Tauch A., Eggeling L., Bathe B., Mockel B., Puhler A.,
RA Kalinowski J.;
RT "Identification and characterization of the last two unknown genes, dapC
RT and dapF, in the succinylase branch of the L-lysine biosynthesis of
RT Corynebacterium glutamicum.";
RL J. Biotechnol. 104:199-211(2003).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS)IN COMPLEX WITH SUBSTRATE, ACTIVE
RP SITE, AND SUBUNIT.
RA Sagong H.-Y., Kim K.-J.;
RT "Crystal strcuture of reduced DapF from Corynebacterium glutamicum.";
RL Submitted (OCT-2016) 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 Involved in the succinylase branch of the diaminopimelate biosynthesis.
CC {ECO:0000269|PubMed:12948639}.
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:12948639};
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:0000269|PubMed:12948639}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|Ref.4}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene are unable transform L,L-
CC DAP and show an impaired growth when supplied with low ammonium but
CC high concentrations of carbon. {ECO:0000269|PubMed:12948639}.
CC -!- SIMILARITY: Belongs to the diaminopimelate epimerase family.
CC {ECO:0000305}.
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DR EMBL; BA000036; BAB99336.1; -; Genomic_DNA.
DR EMBL; BX927153; CAF20284.1; -; Genomic_DNA.
DR RefSeq; NP_601150.1; NC_003450.3.
DR RefSeq; WP_011014772.1; NC_006958.1.
DR PDB; 5H2G; X-ray; 2.00 A; A/B=1-277.
DR PDB; 5H2Y; X-ray; 2.00 A; A/B=1-277.
DR PDB; 5M47; X-ray; 2.59 A; A=1-277.
DR PDBsum; 5H2G; -.
DR PDBsum; 5H2Y; -.
DR PDBsum; 5M47; -.
DR AlphaFoldDB; Q8NP73; -.
DR SMR; Q8NP73; -.
DR STRING; 196627.cg2129; -.
DR KEGG; cgb:cg2129; -.
DR KEGG; cgl:Cgl1943; -.
DR PATRIC; fig|196627.13.peg.1881; -.
DR eggNOG; COG0253; Bacteria.
DR HOGENOM; CLU_053306_4_0_11; -.
DR OMA; HVAMRVH; -.
DR BRENDA; 5.1.1.7; 960.
DR UniPathway; UPA00034; UER00025.
DR Proteomes; UP000000582; 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..277
FT /note="Diaminopimelate epimerase"
FT /id="PRO_0000149837"
FT ACT_SITE 83
FT /note="Proton donor"
FT /evidence="ECO:0000305|Ref.4, ECO:0007744|PDB:5M47"
FT ACT_SITE 221
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 15
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.4, ECO:0007744|PDB:5M47"
FT BINDING 74
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00197"
FT BINDING 84..85
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.4, ECO:0007744|PDB:5M47"
FT BINDING 159
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.4, ECO:0007744|PDB:5M47"
FT BINDING 194
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.4, ECO:0007744|PDB:5M47"
FT BINDING 212..213
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.4, ECO:0007744|PDB:5M47"
FT BINDING 222..223
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.4, ECO:0007744|PDB:5M47"
FT SITE 161
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 212
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 3..12
FT /evidence="ECO:0007829|PDB:5H2G"
FT STRAND 15..21
FT /evidence="ECO:0007829|PDB:5H2G"
FT HELIX 31..38
FT /evidence="ECO:0007829|PDB:5H2G"
FT TURN 40..42
FT /evidence="ECO:0007829|PDB:5H2G"
FT STRAND 47..54
FT /evidence="ECO:0007829|PDB:5H2G"
FT HELIX 55..57
FT /evidence="ECO:0007829|PDB:5H2G"
FT STRAND 67..74
FT /evidence="ECO:0007829|PDB:5H2G"
FT HELIX 86..96
FT /evidence="ECO:0007829|PDB:5H2G"
FT STRAND 99..108
FT /evidence="ECO:0007829|PDB:5H2G"
FT STRAND 114..121
FT /evidence="ECO:0007829|PDB:5H2G"
FT STRAND 123..131
FT /evidence="ECO:0007829|PDB:5H2G"
FT STRAND 136..145
FT /evidence="ECO:0007829|PDB:5H2G"
FT STRAND 148..165
FT /evidence="ECO:0007829|PDB:5H2G"
FT HELIX 171..176
FT /evidence="ECO:0007829|PDB:5H2G"
FT TURN 186..188
FT /evidence="ECO:0007829|PDB:5H2G"
FT STRAND 194..198
FT /evidence="ECO:0007829|PDB:5H2G"
FT STRAND 205..212
FT /evidence="ECO:0007829|PDB:5H2G"
FT TURN 213..215
FT /evidence="ECO:0007829|PDB:5H2G"
FT HELIX 222..235
FT /evidence="ECO:0007829|PDB:5H2G"
FT STRAND 239..247
FT /evidence="ECO:0007829|PDB:5H2G"
FT STRAND 250..257
FT /evidence="ECO:0007829|PDB:5H2G"
FT STRAND 260..277
FT /evidence="ECO:0007829|PDB:5H2G"
SQ SEQUENCE 277 AA; 29203 MW; 41458032D8C7E9DF CRC64;
MNLTIPFAKG HATENDFIII PDEDARLDLT PEMVVTLCDR RAGIGADGIL RVVKAADVEG
STVDPSLWFM DYRNADGSLA EMCGNGVRLF AHWLYSRGLV DNTSFDIGTR AGVRHVDILQ
ADQHSAQVRV DMGIPDVTGL STCDINGQVF AGLGVDMGNP HLACVVPGLS ASALADMELR
APTFDQEFFP HGVNVEIVTE LEDDAVSMRV WERGVGETRS CGTGTVAAAC AALADAGLGE
GTVKVCVPGG EVEVQIFDDG STLTGPSAII ALGEVQI
