DAPDH_BACFN
ID DAPDH_BACFN Reviewed; 299 AA.
AC Q5L9Q6;
DT 16-MAY-2012, integrated into UniProtKB/Swiss-Prot.
DT 21-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 87.
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=BF3481; ORFNames=BF9343_3390;
OS Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019
OS / NCTC 9343 / Onslow).
OC Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Bacteroidaceae;
OC Bacteroides.
OX NCBI_TaxID=272559;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow;
RX PubMed=15746427; DOI=10.1126/science.1107008;
RA Cerdeno-Tarraga A.-M., Patrick S., Crossman L.C., Blakely G., Abratt V.,
RA Lennard N., Poxton I., Duerden B., Harris B., Quail M.A., Barron A.,
RA Clark L., Corton C., Doggett J., Holden M.T.G., Larke N., Line A., Lord A.,
RA Norbertczak H., Ormond D., Price C., Rabbinowitsch E., Woodward J.,
RA Barrell B.G., Parkhill J.;
RT "Extensive DNA inversions in the B. fragilis genome control variable gene
RT expression.";
RL Science 307:1463-1465(2005).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, INDUCTION, AND SUBUNIT.
RC STRAIN=ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / NCTC 9343 / Onslow;
RX PubMed=21616177; DOI=10.1016/j.bbapap.2011.04.019;
RA Hudson A.O., Klartag A., Gilvarg C., Dobson R.C., Marques F.G., Leustek T.;
RT "Dual diaminopimelate biosynthesis pathways in Bacteroides fragilis and
RT Clostridium thermocellum.";
RL Biochim. Biophys. Acta 1814:1162-1168(2011).
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 (m-DAP),
CC since the activity with L,L-2,6-diaminopimelate is less than 5% of the
CC activity observed with m-DAP. Can use NAD(+) only very poorly since the
CC activity observed in the presence of NAD(+) is about 14% of that with
CC NADP(+). {ECO:0000269|PubMed:21616177}.
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;
CC Evidence={ECO:0000269|PubMed:21616177};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.69 mM for L-2-amino-6-oxoheptanedioate (at 30 degrees Celsius
CC and pH 10.5) {ECO:0000269|PubMed:21616177};
CC KM=0.24 mM for NADPH (at 30 degrees Celsius and pH 10.5)
CC {ECO:0000269|PubMed:21616177};
CC KM=4.1 mM for ammonia (at 30 degrees Celsius and pH 10.5)
CC {ECO:0000269|PubMed:21616177};
CC Vmax=0.18 umol/min/mg enzyme for the reductive amination of L-2-
CC amino-6-oxopimelate (at 30 degrees Celsius and pH 10.5)
CC {ECO:0000269|PubMed:21616177};
CC Temperature dependence:
CC Optimum temperature is 37 degrees Celsius.
CC {ECO:0000269|PubMed:21616177};
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:21616177}.
CC -!- INDUCTION: Is expressed at a very high level and is reciprocally
CC regulated with dapL and dapF. {ECO:0000269|PubMed:21616177}.
CC -!- SIMILARITY: Belongs to the diaminopimelate dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; CR626927; CAH09171.1; -; Genomic_DNA.
DR RefSeq; WP_005790557.1; NC_003228.3.
DR AlphaFoldDB; Q5L9Q6; -.
DR SMR; Q5L9Q6; -.
DR STRING; 272559.BF9343_3390; -.
DR EnsemblBacteria; CAH09171; CAH09171; BF9343_3390.
DR GeneID; 66331676; -.
DR KEGG; bfs:BF9343_3390; -.
DR eggNOG; COG0673; Bacteria.
DR HOGENOM; CLU_055796_1_0_10; -.
DR OMA; WDPGLFS; -.
DR OrthoDB; 803114at2; -.
DR BioCyc; BFRA272559:G1GHZ-3704-MON; -.
DR UniPathway; UPA00034; UER00026.
DR Proteomes; UP000006731; Chromosome.
DR GO; GO:0047850; F:diaminopimelate dehydrogenase activity; IEA:UniProtKB-EC.
DR GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
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 InterPro; IPR010190; Diaminopimelate_DH_Ddh.
DR InterPro; IPR000683; Gfo/Idh/MocA-like_OxRdtase_N.
DR InterPro; IPR032094; Meso-DAP_DH_C.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR Pfam; PF16654; DAPDH_C; 1.
DR Pfam; PF01408; GFO_IDH_MocA; 1.
DR PIRSF; PIRSF025648; DDH; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR TIGRFAMs; TIGR01921; DAP-DH; 1.
PE 1: Evidence at protein level;
KW Amino-acid biosynthesis; Diaminopimelate biosynthesis; Lysine biosynthesis;
KW NADP; Oxidoreductase; Reference proteome.
FT CHAIN 1..299
FT /note="Meso-diaminopimelate D-dehydrogenase"
FT /id="PRO_0000417122"
FT BINDING 11..14
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 36
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 67..70
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 90..92
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 92
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 119..123
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 122
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 146
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 152..153
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 171
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 181
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 227
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 253
FT /ligand="substrate"
FT /evidence="ECO:0000250"
SQ SEQUENCE 299 AA; 32327 MW; 353A226C30E3A658 CRC64;
MKKVRAAIVG YGNIGRYVLE ALQAAPDFEI AGVVRRAGAE NKPAELNDYA VVKDIKELQG
VDVAILCTPT RSVEKYAKEI LAMGINTVDS FDIHTGIVDL RRELGACAKE HGAVSIISAG
WDPGSDSIVR TMLEAIAPKG ITYTNFGPGM SMGHTVAVKA IDGVKAALSM TIPTGTGIHR
RMVYIELKDG YKFEEVAAAI KSDAYFVNDE THVKQVPSVD ALLDMGHGVN LTRKGVSGKT
QNQLFEFNMR INNPALTAQV LVCVARASMK QQPGCYTMVE VPVIDLLPGD REEWIGHLV
