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 27-MAR-2024, entry version 116. 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}; GN OrderedLocusNames=Cgl1943, cg2129; OS Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / OS JCM 1318 / LMG 3730 / NCIMB 10025). OC Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; OC Corynebacteriaceae; 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 / RC NCIMB 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 / RC NCIMB 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 / RC NCIMB 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 to transform CC L,L-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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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 OrthoDB; 9805408at2; -. DR BioCyc; CORYNE:G18NG-11535-MONOMER; -. DR BRENDA; 5.1.1.7; 960. DR UniPathway; UPA00034; UER00025. DR Proteomes; UP000000582; Chromosome. DR Proteomes; UP000001009; 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 NCBIfam; TIGR00652; DapF; 1. DR PANTHER; PTHR31689:SF0; DIAMINOPIMELATE EPIMERASE; 1. DR PANTHER; PTHR31689; DIAMINOPIMELATE EPIMERASE, CHLOROPLASTIC; 1. DR Pfam; PF01678; DAP_epimerase; 2. DR SUPFAM; SSF54506; Diaminopimelate epimerase-like; 2. 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 //