ID DAPB_VIBVU Reviewed; 269 AA.
AC Q8DEM0;
DT 15-AUG-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 27-MAR-2024, entry version 132.
DE RecName: Full=4-hydroxy-tetrahydrodipicolinate reductase {ECO:0000255|HAMAP-Rule:MF_00102};
DE Short=HTPA reductase {ECO:0000255|HAMAP-Rule:MF_00102};
DE EC=1.17.1.8 {ECO:0000255|HAMAP-Rule:MF_00102};
GN Name=dapB {ECO:0000255|HAMAP-Rule:MF_00102}; OrderedLocusNames=VV1_0567;
OS Vibrio vulnificus (strain CMCP6).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=216895;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CMCP6;
RA Rhee J.H., Kim S.Y., Chung S.S., Kim J.J., Moon Y.H., Jeong H., Choy H.E.;
RT "Complete genome sequence of Vibrio vulnificus CMCP6.";
RL Submitted (DEC-2002) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate
CC (HTPA) to tetrahydrodipicolinate. {ECO:0000255|HAMAP-Rule:MF_00102}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-2,3,4,5-tetrahydrodipicolinate + H2O + NAD(+) = (2S,4S)-4-
CC hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADH;
CC Xref=Rhea:RHEA:35323, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16845, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945,
CC ChEBI:CHEBI:67139; EC=1.17.1.8; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00102};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-2,3,4,5-tetrahydrodipicolinate + H2O + NADP(+) = (2S,4S)-
CC 4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H(+) + NADPH;
CC Xref=Rhea:RHEA:35331, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16845, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349,
CC ChEBI:CHEBI:67139; EC=1.17.1.8; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00102};
CC -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via DAP
CC pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 4/4.
CC {ECO:0000255|HAMAP-Rule:MF_00102}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00102}.
CC -!- SIMILARITY: Belongs to the DapB family. {ECO:0000255|HAMAP-
CC Rule:MF_00102}.
CC -!- CAUTION: Was originally thought to be a dihydrodipicolinate reductase
CC (DHDPR), catalyzing the conversion of dihydrodipicolinate to
CC tetrahydrodipicolinate. However, it was shown in E.coli that the
CC substrate of the enzymatic reaction is not dihydrodipicolinate (DHDP)
CC but in fact (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid
CC (HTPA), the product released by the DapA-catalyzed reaction.
CC {ECO:0000305}.
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DR EMBL; AE016795; AAO09084.1; -; Genomic_DNA.
DR RefSeq; WP_011078654.1; NC_004459.3.
DR PDB; 5TEJ; X-ray; 2.50 A; A/B/C/D=1-269.
DR PDB; 5TEM; X-ray; 2.20 A; A/C=1-269.
DR PDB; 5TEN; X-ray; 2.45 A; A/B/C/D/E/F/G/H=1-269.
DR PDB; 5US6; X-ray; 2.61 A; A/B/C/D/E/F/G/H/I/J/K/L=1-269.
DR PDBsum; 5TEJ; -.
DR PDBsum; 5TEM; -.
DR PDBsum; 5TEN; -.
DR PDBsum; 5US6; -.
DR AlphaFoldDB; Q8DEM0; -.
DR SMR; Q8DEM0; -.
DR KEGG; vvu:VV1_0567; -.
DR HOGENOM; CLU_047479_2_1_6; -.
DR UniPathway; UPA00034; UER00018.
DR Proteomes; UP000002275; Chromosome 1.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0008839; F:4-hydroxy-tetrahydrodipicolinate reductase; IEA:UniProtKB-EC.
DR GO; GO:0051287; F:NAD binding; IEA:UniProtKB-UniRule.
DR GO; GO:0050661; F:NADP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016726; F:oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor; IEA:UniProtKB-UniRule.
DR GO; GO:0019877; P:diaminopimelate biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.50.720; NAD(P)-binding Rossmann-like Domain; 1.
DR HAMAP; MF_00102; DapB; 1.
DR InterPro; IPR022663; DapB_C.
DR InterPro; IPR000846; DapB_N.
DR InterPro; IPR022664; DapB_N_CS.
DR InterPro; IPR023940; DHDPR_bac.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR NCBIfam; TIGR00036; dapB; 1.
DR PANTHER; PTHR20836:SF0; 4-HYDROXY-TETRAHYDRODIPICOLINATE REDUCTASE 1, CHLOROPLASTIC-RELATED; 1.
DR PANTHER; PTHR20836; DIHYDRODIPICOLINATE REDUCTASE; 1.
DR Pfam; PF05173; DapB_C; 1.
DR Pfam; PF01113; DapB_N; 1.
DR PIRSF; PIRSF000161; DHPR; 1.
DR SUPFAM; SSF55347; Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain; 1.
DR SUPFAM; SSF51735; NAD(P)-binding Rossmann-fold domains; 1.
DR PROSITE; PS01298; DAPB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Cytoplasm;
KW Diaminopimelate biosynthesis; Lysine biosynthesis; NAD; NADP;
KW Oxidoreductase.
FT CHAIN 1..269
FT /note="4-hydroxy-tetrahydrodipicolinate reductase"
FT /id="PRO_0000141506"
FT ACT_SITE 155
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00102"
FT ACT_SITE 159
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00102"
FT BINDING 8..13
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00102"
FT BINDING 34
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00102"
FT BINDING 35
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00102"
FT BINDING 98..100
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00102"
FT BINDING 122..125
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00102"
FT BINDING 156
FT /ligand="(S)-2,3,4,5-tetrahydrodipicolinate"
FT /ligand_id="ChEBI:CHEBI:16845"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00102"
FT BINDING 165..166
FT /ligand="(S)-2,3,4,5-tetrahydrodipicolinate"
FT /ligand_id="ChEBI:CHEBI:16845"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00102"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:5TEM"
FT TURN 8..10
FT /evidence="ECO:0007829|PDB:5TEM"
FT HELIX 12..23
FT /evidence="ECO:0007829|PDB:5TEM"
FT STRAND 27..33
FT /evidence="ECO:0007829|PDB:5TEM"
FT TURN 39..42
FT /evidence="ECO:0007829|PDB:5TEM"
FT HELIX 46..48
FT /evidence="ECO:0007829|PDB:5TEM"
FT STRAND 57..60
FT /evidence="ECO:0007829|PDB:5TEM"
FT HELIX 62..68
FT /evidence="ECO:0007829|PDB:5TEM"
FT STRAND 70..74
FT /evidence="ECO:0007829|PDB:5TEM"
FT HELIX 78..91
FT /evidence="ECO:0007829|PDB:5TEM"
FT STRAND 94..97
FT /evidence="ECO:0007829|PDB:5TEM"
FT HELIX 104..113
FT /evidence="ECO:0007829|PDB:5TEM"
FT TURN 114..116
FT /evidence="ECO:0007829|PDB:5TEM"
FT STRAND 117..121
FT /evidence="ECO:0007829|PDB:5TEM"
FT HELIX 127..143
FT /evidence="ECO:0007829|PDB:5TEM"
FT TURN 144..146
FT /evidence="ECO:0007829|PDB:5TEM"
FT STRAND 147..155
FT /evidence="ECO:0007829|PDB:5TEM"
FT STRAND 161..163
FT /evidence="ECO:0007829|PDB:5TEM"
FT HELIX 165..177
FT /evidence="ECO:0007829|PDB:5TEM"
FT HELIX 182..185
FT /evidence="ECO:0007829|PDB:5TEM"
FT STRAND 202..208
FT /evidence="ECO:0007829|PDB:5TEM"
FT STRAND 214..221
FT /evidence="ECO:0007829|PDB:5TEM"
FT STRAND 226..233
FT /evidence="ECO:0007829|PDB:5TEM"
FT HELIX 237..250
FT /evidence="ECO:0007829|PDB:5TEM"
FT STRAND 255..258
FT /evidence="ECO:0007829|PDB:5TEM"
FT HELIX 260..264
FT /evidence="ECO:0007829|PDB:5TEM"
SQ SEQUENCE 269 AA; 28639 MW; B8C741BDCC604C56 CRC64;
MVRIAVAGAA GRMGRNLVKA AHHNPVAKVA AGSERPESSL VGVDLGELCG EGKFDVVVCD
DLAKQIDQFD VIIDFTAPAS TLNNLALCQQ YGKSIVIGTT GFTEEQREQI DLVAQQVPVV
MAPNYSVGVN LVFKLLEKAA KVMGDYCDIE IVEAHHRHKV DAPSGTAIGM GEAIAGAMGN
KLSDVAVYAR EGITGERTKD EIGFATIRAG DIVGEHTAMF ADIGERVEIT HKATDRMTFA
NGAVKAAVWL HEKPAGFYTM TDVLGLNDL
//
