ID DAPDH_CORGL Reviewed; 320 AA.
AC P04964;
DT 13-AUG-1987, integrated into UniProtKB/Swiss-Prot.
DT 13-AUG-1987, sequence version 1.
DT 27-MAR-2024, entry version 160.
DE RecName: Full=Meso-diaminopimelate D-dehydrogenase;
DE Short=DAPDH;
DE Short=Meso-DAP dehydrogenase;
DE EC=1.4.1.16;
GN Name=ddh; OrderedLocusNames=Cgl2617, cg2900;
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 [GENOMIC DNA].
RC STRAIN=KY 10755;
RX PubMed=3588313; DOI=10.1093/nar/15.9.3917;
RA Ishino S., Mizukami T., Yamaguchi K., Katsumata R., Araki K.;
RT "Nucleotide sequence of the meso-diaminopimelate D-dehydrogenase gene from
RT Corynebacterium glutamicum.";
RL Nucleic Acids Res. 15:3917-3917(1987).
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=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 [3]
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 [4]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, ACTIVITY REGULATION, AND SUBUNIT.
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RA Misono H., Ogasawara M., Nagasaki S.;
RT "Characterization of meso-diaminopimelate dehydrogenase from
RT Corynebacterium glutamicum.";
RL Agric. Biol. Chem. 50:2729-2734(1986).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, CRYSTALLIZATION, MASS SPECTROMETRY, AND
RP SUBUNIT.
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=8865347; DOI=10.1002/prot.12;
RA Reddy S.G., Scapin G., Blanchard J.S.;
RT "Expression, purification, and crystallization of meso-diaminopimelate
RT dehydrogenase from Corynebacterium glutamicum.";
RL Proteins 25:514-516(1996).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEX WITH NADP(+), DOMAIN, AND
RP SUBUNIT.
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=8885833; DOI=10.1021/bi961628i;
RA Scapin G., Reddy S.G., Blanchard J.S.;
RT "Three-dimensional structure of meso-diaminopimelic acid dehydrogenase from
RT Corynebacterium glutamicum.";
RL Biochemistry 35:13540-13551(1996).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) IN COMPLEXES WITH
RP MESO-2,6-DIAMINOPIMELATE; NADP(+) AND AN ISOXAZOLINE INHIBITOR, AND
RP SUBUNIT.
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=9521647; DOI=10.1021/bi9727949;
RA Scapin G., Cirilli M., Reddy S.G., Gao Y., Vederas J.C., Blanchard J.S.;
RT "Substrate and inhibitor binding sites in Corynebacterium glutamicum
RT diaminopimelate dehydrogenase.";
RL Biochemistry 37:3278-3285(1998).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH NADP(+) AND
RP SUBSTRATE ANALOG INHIBITOR, AND SUBUNIT.
RC STRAIN=ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB
RC 10025;
RX PubMed=11106178; DOI=10.1110/ps.9.10.2034;
RA Cirilli M., Scapin G., Sutherland A., Vederas J.C., Blanchard J.S.;
RT "The three-dimensional structure of the ternary complex of Corynebacterium
RT glutamicum diaminopimelate dehydrogenase-NADPH-L-2-amino-6-methylene-
RT pimelate.";
RL Protein Sci. 9:2034-2037(2000).
CC -!- FUNCTION: Catalyzes the reversible NADPH-dependent reductive amination
CC of L-2-amino-6-oxopimelate, the acyclic form of L-
CC tetrahydrodipicolinate, to generate the meso compound, D,L-2,6-
CC diaminopimelate. Probably plays a role in lysine biosynthesis. Exhibits
CC a high substrate specificity for meso-2,6-diaminopimelate, since L,L-
CC 2,6-diaminopimelate, D,D-2,6-diaminopimelate, L-glutamate, L-alanine,
CC L-leucine, L-valine, L-aspartate, L-threonine, L-homoserine, L-
CC methionine, L-lysine, L-serine, L-phenylalanine, L-tyrosine, L-
CC tryptophan, L-ornithine, L-histidine, L-arginine, D-glutamate, and D-
CC alanine are not substrates for the oxidative deamination reaction. Can
CC use NAD(+) only poorly since the activity observed in the presence of
CC NAD(+) is about 3% of that with NADP(+). {ECO:0000269|PubMed:8865347,
CC ECO:0000269|Ref.4}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + meso-2,6-diaminoheptanedioate + NADP(+) = (S)-2-amino-6-
CC oxoheptanedioate + H(+) + NADPH + NH4(+); Xref=Rhea:RHEA:13561,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:57783, ChEBI:CHEBI:57791, ChEBI:CHEBI:58349,
CC ChEBI:CHEBI:58556; EC=1.4.1.16; Evidence={ECO:0000269|PubMed:8865347,
CC ECO:0000269|Ref.4};
CC -!- ACTIVITY REGULATION: L,L-2,6-diaminopimelate and D,D-2,6-
CC diaminopimelate competitively inhibit the oxidative deamination of
CC meso-2,6-diaminopimelate. The enzyme is also inhibited by L-cysteine,
CC and by p-chloromercuribenzoate, iodoacetic acid and HgCl(2) in vitro.
CC {ECO:0000269|Ref.4}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=3.1 mM for meso-2,6-diaminoheptanedioate {ECO:0000269|Ref.4};
CC KM=0.12 mM for NADP(+) {ECO:0000269|Ref.4};
CC KM=0.13 mM for NADPH {ECO:0000269|Ref.4};
CC KM=0.28 mM for L-2-amino-6-oxoheptanedioate {ECO:0000269|Ref.4};
CC KM=36 mM for ammonia {ECO:0000269|Ref.4};
CC pH dependence:
CC Optimum pH is about 9.8 for the oxidative deamination of meso-
CC diaminopimelate and 7.9 for the reductive amination of L-2-amino-6-
CC oxopimelate. {ECO:0000269|Ref.4};
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC pathway; DL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate: step
CC 1/1.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:11106178,
CC ECO:0000269|PubMed:8865347, ECO:0000269|PubMed:8885833,
CC ECO:0000269|PubMed:9521647, ECO:0000269|Ref.4}.
CC -!- DOMAIN: Is composed of three domains: a dinucleotide binding domain, a
CC dimerization domain, and a substrate-binding domain.
CC {ECO:0000269|PubMed:8885833}.
CC -!- MASS SPECTROMETRY: Mass=35198; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:8865347};
CC -!- SIMILARITY: Belongs to the diaminopimelate dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; Y00151; CAA68346.1; -; Genomic_DNA.
DR EMBL; BA000036; BAC00011.1; -; Genomic_DNA.
DR EMBL; BX927155; CAF21279.1; -; Genomic_DNA.
DR PIR; S07384; S07384.
DR RefSeq; NP_601818.2; NC_003450.3.
DR RefSeq; WP_011015254.1; NC_006958.1.
DR PDB; 1DAP; X-ray; 2.20 A; A/B=1-320.
DR PDB; 1F06; X-ray; 2.10 A; A/B=1-320.
DR PDB; 2DAP; X-ray; 2.20 A; A=1-320.
DR PDB; 3DAP; X-ray; 2.20 A; A/B=1-320.
DR PDB; 5LOA; X-ray; 1.84 A; A/B=2-320.
DR PDB; 5LOC; X-ray; 2.04 A; A/B=2-320.
DR PDBsum; 1DAP; -.
DR PDBsum; 1F06; -.
DR PDBsum; 2DAP; -.
DR PDBsum; 3DAP; -.
DR PDBsum; 5LOA; -.
DR PDBsum; 5LOC; -.
DR AlphaFoldDB; P04964; -.
DR SMR; P04964; -.
DR STRING; 196627.cg2900; -.
DR DrugBank; DB03590; 2,6-Diaminopimelic Acid.
DR DrugBank; DB02892; L-2-Amino-6-Methylene-Pimelic Acid.
DR World-2DPAGE; 0001:P04964; -.
DR KEGG; cgb:cg2900; -.
DR KEGG; cgl:Cgl2617; -.
DR PATRIC; fig|196627.13.peg.2553; -.
DR eggNOG; COG1748; Bacteria.
DR HOGENOM; CLU_055796_0_0_11; -.
DR OrthoDB; 9774191at2; -.
DR BioCyc; CORYNE:G18NG-12233-MONOMER; -.
DR BioCyc; MetaCyc:MONOMER-6621; -.
DR BRENDA; 1.4.1.16; 960.
DR UniPathway; UPA00034; UER00026.
DR EvolutionaryTrace; P04964; -.
DR Proteomes; UP000000582; Chromosome.
DR Proteomes; UP000001009; Chromosome.
DR GO; GO:0047850; F:diaminopimelate dehydrogenase activity; IEA:UniProtKB-EC.
DR GO; GO:0019877; P:diaminopimelate biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.40.50.720; NAD(P)-binding Rossmann-like Domain; 1.
DR InterPro; IPR010190; Diaminopimelate_DH_Ddh.
DR InterPro; IPR032094; Meso-DAP_DH_C.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR NCBIfam; TIGR01921; DAP-DH; 1.
DR Pfam; PF16654; DAPDH_C; 1.
DR PIRSF; PIRSF025648; DDH; 1.
DR SUPFAM; SSF55347; Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain; 1.
DR SUPFAM; SSF51735; NAD(P)-binding Rossmann-fold domains; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Diaminopimelate biosynthesis;
KW Lysine biosynthesis; NADP; Oxidoreductase; Reference proteome.
FT CHAIN 1..320
FT /note="Meso-diaminopimelate D-dehydrogenase"
FT /id="PRO_0000079848"
FT BINDING 11..14
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 35..37
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 65..68
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 88..90
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 90
FT /ligand="substrate"
FT BINDING 117..121
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 120
FT /ligand="substrate"
FT BINDING 144
FT /ligand="substrate"
FT BINDING 150..151
FT /ligand="substrate"
FT BINDING 169
FT /ligand="substrate"
FT BINDING 195
FT /ligand="substrate"
FT BINDING 244
FT /ligand="substrate"
FT BINDING 270
FT /ligand="substrate"
FT STRAND 4..9
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 13..22
FT /evidence="ECO:0007829|PDB:5LOA"
FT STRAND 28..38
FT /evidence="ECO:0007829|PDB:5LOA"
FT STRAND 41..44
FT /evidence="ECO:0007829|PDB:5LOA"
FT STRAND 46..48
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 52..55
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 56..58
FT /evidence="ECO:0007829|PDB:5LOA"
FT STRAND 60..64
FT /evidence="ECO:0007829|PDB:5LOA"
FT TURN 68..70
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 71..79
FT /evidence="ECO:0007829|PDB:5LOA"
FT TURN 80..82
FT /evidence="ECO:0007829|PDB:5LOA"
FT STRAND 83..86
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 92..94
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 95..109
FT /evidence="ECO:0007829|PDB:5LOA"
FT STRAND 112..114
FT /evidence="ECO:0007829|PDB:5LOA"
FT TURN 119..122
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 123..134
FT /evidence="ECO:0007829|PDB:5LOA"
FT STRAND 135..137
FT /evidence="ECO:0007829|PDB:1DAP"
FT STRAND 139..144
FT /evidence="ECO:0007829|PDB:5LOA"
FT STRAND 146..148
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 150..157
FT /evidence="ECO:0007829|PDB:5LOA"
FT STRAND 163..171
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 173..180
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 189..192
FT /evidence="ECO:0007829|PDB:5LOA"
FT STRAND 193..200
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 203..205
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 206..214
FT /evidence="ECO:0007829|PDB:5LOA"
FT TURN 217..222
FT /evidence="ECO:0007829|PDB:5LOA"
FT STRAND 225..229
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 232..238
FT /evidence="ECO:0007829|PDB:5LOA"
FT STRAND 239..242
FT /evidence="ECO:0007829|PDB:3DAP"
FT STRAND 244..256
FT /evidence="ECO:0007829|PDB:5LOA"
FT STRAND 258..269
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 270..290
FT /evidence="ECO:0007829|PDB:5LOA"
FT STRAND 295..297
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 299..301
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 304..307
FT /evidence="ECO:0007829|PDB:5LOA"
FT HELIX 312..319
FT /evidence="ECO:0007829|PDB:5LOA"
SQ SEQUENCE 320 AA; 35199 MW; D29D3EB6DFDA35DE CRC64;
MTNIRVAIVG YGNLGRSVEK LIAKQPDMDL VGIFSRRATL DTKTPVFDVA DVDKHADDVD
VLFLCMGSAT DIPEQAPKFA QFACTVDTYD NHRDIPRHRQ VMNEAATAAG NVALVSTGWD
PGMFSINRVY AAAVLAEHQQ HTFWGPGLSQ GHSDALRRIP GVQKAVQYTL PSEDALEKAR
RGEAGDLTGK QTHKRQCFVV ADAADHERIE NDIRTMPDYF VGYEVEVNFI DEATFDSEHT
GMPHGGHVIT TGDTGGFNHT VEYILKLDRN PDFTASSQIA FGRAAHRMKQ QGQSGAFTVL
EVAPYLLSPE NLDDLIARDV
//
