DAPDH_URETH
ID DAPDH_URETH Reviewed; 326 AA.
AC G1UII1;
DT 16-MAY-2012, integrated into UniProtKB/Swiss-Prot.
DT 16-NOV-2011, sequence version 1.
DT 03-AUG-2022, entry version 34.
DE RecName: Full=Meso-diaminopimelate D-dehydrogenase;
DE Short=DAPDH;
DE Short=Meso-DAP dehydrogenase;
DE EC=1.4.1.16;
GN Name=ddh;
OS Ureibacillus thermosphaericus.
OC Bacteria; Firmicutes; Bacilli; Bacillales; Planococcaceae; Ureibacillus.
OX NCBI_TaxID=51173;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-11, FUNCTION,
RP CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL PROPERTIES,
RP ACTIVITY REGULATION, AND SUBUNIT.
RC STRAIN=A1 / NBRC 108682;
RX PubMed=22117688; DOI=10.1186/2191-0855-1-43;
RA Akita H., Fujino Y., Doi K., Ohshima T.;
RT "Highly stable meso-diaminopimelate dehydrogenase from an Ureibacillus
RT thermosphaericus strain A1 isolated from a Japanese compost: purification,
RT characterization and sequencing.";
RL AMB Express 1:43-43(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. Is
CC highly specific for meso-2,6-diaminopimelate as the electron donor,
CC since the following amino acids are inert for the oxidative deamination
CC reaction: DL-2-aminopimelate, D-glutamate, L-glutamate, D-aspartate, L-
CC aspartate, D-alanine, L-alanine, D-valine, L-valine, D-lysine, L-
CC lysine, D-phenylalanine, L-phenylalanine, D-leucine, L-leucine, D-
CC threonine, L-threonine, D-serine, L-serine, D-tryptophan, L-tryptophan,
CC D-cysteine, L-cysteine, D-histidine, L-histidine, D-methionine, D-
CC arginine, D-proline, D-asparagine, D-glutamine, D-isoleucine and D-
CC ornithine. Moreover, exclusively uses NADP as the electron acceptor for
CC the oxidative deamination of meso-DAP; NAD is inert.
CC {ECO:0000269|PubMed:22117688}.
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:22117688};
CC -!- ACTIVITY REGULATION: The enzyme is completely inhibited by p-
CC chloromercuribenzoate and HgCl(2) in vitro. Thioglycollate, L-cysteine
CC and Cu(2+) also strongly inhibit the enzyme.
CC {ECO:0000269|PubMed:22117688}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.6 mM for meso-2,6-diaminoheptanedioate (at 50 degrees Celsius
CC and pH 10.5) {ECO:0000269|PubMed:22117688};
CC KM=0.13 mM for NADP(+) (at 50 degrees Celsius and pH 10.5)
CC {ECO:0000269|PubMed:22117688};
CC pH dependence:
CC Optimum pH is about 10.5. No activity is lost after 30 minutes
CC incubation at pHs between 5.0 and 11.0.
CC {ECO:0000269|PubMed:22117688};
CC Temperature dependence:
CC Optimum temperature is 65 degrees Celsius. Thermostable. No activity
CC is lost after 30 minutes incubation at temperatures below 60 degrees
CC Celsius, while half of the activity is lost after 30 minutes
CC incubation at 65 degrees Celsius. {ECO:0000269|PubMed:22117688};
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:22117688}.
CC -!- SIMILARITY: Belongs to the diaminopimelate dehydrogenase family.
CC {ECO:0000305}.
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DR EMBL; AB636161; BAK86217.1; -; Genomic_DNA.
DR RefSeq; WP_016838077.1; NZ_JAAXPW010000008.1.
DR PDB; 3WYB; X-ray; 2.40 A; A/B=1-326.
DR PDB; 3WYC; X-ray; 2.07 A; A/B=1-326.
DR PDB; 5GZ1; X-ray; 1.78 A; A/B=1-326.
DR PDB; 5GZ3; X-ray; 1.59 A; A/B=1-326.
DR PDB; 5GZ6; X-ray; 1.74 A; A/B=1-326.
DR PDBsum; 3WYB; -.
DR PDBsum; 3WYC; -.
DR PDBsum; 5GZ1; -.
DR PDBsum; 5GZ3; -.
DR PDBsum; 5GZ6; -.
DR AlphaFoldDB; G1UII1; -.
DR SMR; G1UII1; -.
DR BRENDA; 1.4.1.16; 13484.
DR UniPathway; UPA00034; UER00026.
DR GO; GO:0008839; F:4-hydroxy-tetrahydrodipicolinate reductase; IEA:InterPro.
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 InterPro; IPR000846; DapB_N.
DR InterPro; IPR010190; Diaminopimelate_DH_Ddh.
DR InterPro; IPR032094; Meso-DAP_DH_C.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR Pfam; PF01113; DapB_N; 1.
DR Pfam; PF16654; DAPDH_C; 1.
DR PIRSF; PIRSF025648; DDH; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR TIGRFAMs; TIGR01921; DAP-DH; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Diaminopimelate biosynthesis;
KW Direct protein sequencing; Lysine biosynthesis; NADP; Oxidoreductase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:22117688"
FT CHAIN 2..326
FT /note="Meso-diaminopimelate D-dehydrogenase"
FT /id="PRO_0000417121"
FT BINDING 11..14
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 35..37
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 69..72
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 92..94
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 94
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 121..125
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 124
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 148
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 154..155
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 173
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 199
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 249
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 276
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT STRAND 4..9
FT /evidence="ECO:0007829|PDB:5GZ3"
FT HELIX 13..22
FT /evidence="ECO:0007829|PDB:5GZ3"
FT STRAND 28..37
FT /evidence="ECO:0007829|PDB:5GZ3"
FT HELIX 39..41
FT /evidence="ECO:0007829|PDB:5GZ3"
FT STRAND 45..47
FT /evidence="ECO:0007829|PDB:5GZ6"
FT STRAND 49..52
FT /evidence="ECO:0007829|PDB:5GZ3"
FT HELIX 53..59
FT /evidence="ECO:0007829|PDB:5GZ3"
FT TURN 60..62
FT /evidence="ECO:0007829|PDB:5GZ3"
FT STRAND 64..68
FT /evidence="ECO:0007829|PDB:5GZ3"
FT TURN 72..74
FT /evidence="ECO:0007829|PDB:5GZ3"
FT HELIX 75..84
FT /evidence="ECO:0007829|PDB:5GZ3"
FT STRAND 87..91
FT /evidence="ECO:0007829|PDB:5GZ3"
FT HELIX 96..98
FT /evidence="ECO:0007829|PDB:5GZ3"
FT HELIX 99..113
FT /evidence="ECO:0007829|PDB:5GZ3"
FT STRAND 116..118
FT /evidence="ECO:0007829|PDB:5GZ3"
FT TURN 123..126
FT /evidence="ECO:0007829|PDB:5GZ3"
FT HELIX 127..138
FT /evidence="ECO:0007829|PDB:5GZ3"
FT STRAND 140..148
FT /evidence="ECO:0007829|PDB:5GZ3"
FT STRAND 150..152
FT /evidence="ECO:0007829|PDB:5GZ3"
FT HELIX 154..161
FT /evidence="ECO:0007829|PDB:5GZ3"
FT STRAND 166..175
FT /evidence="ECO:0007829|PDB:5GZ3"
FT HELIX 177..184
FT /evidence="ECO:0007829|PDB:5GZ3"
FT HELIX 193..196
FT /evidence="ECO:0007829|PDB:5GZ3"
FT STRAND 197..205
FT /evidence="ECO:0007829|PDB:5GZ3"
FT HELIX 211..219
FT /evidence="ECO:0007829|PDB:5GZ3"
FT TURN 222..227
FT /evidence="ECO:0007829|PDB:5GZ3"
FT STRAND 230..234
FT /evidence="ECO:0007829|PDB:5GZ3"
FT HELIX 237..243
FT /evidence="ECO:0007829|PDB:5GZ3"
FT STRAND 244..246
FT /evidence="ECO:0007829|PDB:5GZ6"
FT STRAND 249..258
FT /evidence="ECO:0007829|PDB:5GZ3"
FT STRAND 264..275
FT /evidence="ECO:0007829|PDB:5GZ3"
FT HELIX 276..296
FT /evidence="ECO:0007829|PDB:5GZ3"
FT STRAND 301..303
FT /evidence="ECO:0007829|PDB:5GZ3"
FT HELIX 305..307
FT /evidence="ECO:0007829|PDB:5GZ3"
FT HELIX 310..313
FT /evidence="ECO:0007829|PDB:5GZ3"
FT STRAND 314..316
FT /evidence="ECO:0007829|PDB:5GZ3"
FT HELIX 318..324
FT /evidence="ECO:0007829|PDB:5GZ3"
SQ SEQUENCE 326 AA; 36010 MW; DE4ECDE239F7A3BB CRC64;
MSKIRIGIVG YGNLGRGVEA AIQQNPDMEL VAVFTRRDPK TVAVKSNVKV LHVDDAQSYK
DEIDVMILCG GSATDLPEQG PYFAQYFNTI DSFDTHARIP DYFDAVNAAA EQSGKVAIIS
VGWDPGLFSL NRLLGEVVLP VGNTYTFWGK GVSQGHSDAI RRIQGVKNAV QYTIPIDEAV
NRVRSGENPE LSTREKHARE CFVVLEEGAD PAKVEHEIKT MPNYFDEYDT TVHFISEEEL
KQNHSGMPHG GFVIRSGKSD EGHKQIIEFS LNLESNPMFT SSALVAYARA AYRLSQNGDK
GAKTVFDIPF GLLSPKSPED LRKELL
