DAPB_THEMA
ID DAPB_THEMA Reviewed; 216 AA.
AC Q9X1K8;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1999, sequence version 1.
DT 03-AUG-2022, entry version 149.
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=TM_1520;
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.27 ANGSTROMS) IN COMPLEX WITH NADH, FUNCTION,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, ACTIVITY REGULATION,
RP AND SUBUNIT.
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=18250105; DOI=10.1093/jb/mvn012;
RA Pearce F.G., Sprissler C., Gerrard J.A.;
RT "Characterization of dihydrodipicolinate reductase from Thermotoga maritima
RT reveals evolution of substrate binding kinetics.";
RL J. Biochem. 143:617-623(2008).
CC -!- FUNCTION: Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate
CC (HTPA) to tetrahydrodipicolinate (Probable). Uses NADPH as a reductant
CC with much more efficiency than NADH. {ECO:0000255|HAMAP-Rule:MF_00102,
CC ECO:0000269|PubMed:18250105, ECO:0000305}.
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 -!- ACTIVITY REGULATION: Is inhibited by high concentrations of NADH.
CC {ECO:0000269|PubMed:18250105}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=2.5 uM for NADH (at 30 degrees Celsius)
CC {ECO:0000269|PubMed:18250105};
CC KM=0.6 uM for NADPH (at 30 degrees Celsius)
CC {ECO:0000269|PubMed:18250105};
CC KM=1.8 uM for NADH (at 45 degrees Celsius)
CC {ECO:0000269|PubMed:18250105};
CC KM=2.1 uM for NADPH (at 45 degrees Celsius)
CC {ECO:0000269|PubMed:18250105};
CC Temperature dependence:
CC Is stable for up to 48 hours at 80 degrees Celsius. Has a thermal
CC denaturation midpoint (Tm) of 95.7 degrees Celsius.
CC {ECO:0000269|PubMed:18250105};
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 -!- SUBUNIT: Homotetramer. {ECO:0000305|PubMed:18250105}.
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; AE000512; AAD36587.1; -; Genomic_DNA.
DR PIR; A72246; A72246.
DR RefSeq; NP_229320.1; NC_000853.1.
DR RefSeq; WP_004081877.1; NZ_CP011107.1.
DR PDB; 1VM6; X-ray; 2.27 A; A/B/C/D=1-216.
DR PDBsum; 1VM6; -.
DR AlphaFoldDB; Q9X1K8; -.
DR SMR; Q9X1K8; -.
DR STRING; 243274.THEMA_06700; -.
DR EnsemblBacteria; AAD36587; AAD36587; TM_1520.
DR KEGG; tma:TM1520; -.
DR eggNOG; COG0289; Bacteria.
DR InParanoid; Q9X1K8; -.
DR OMA; HHPNKAD; -.
DR OrthoDB; 803114at2; -.
DR BRENDA; 1.17.1.8; 6331.
DR UniPathway; UPA00034; UER00018.
DR EvolutionaryTrace; Q9X1K8; -.
DR Proteomes; UP000008183; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0008839; F:4-hydroxy-tetrahydrodipicolinate reductase; IBA:GO_Central.
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; IBA:GO_Central.
DR GO; GO:0009089; P:lysine biosynthetic process via diaminopimelate; IEA:UniProtKB-UniRule.
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 PANTHER; PTHR20836; PTHR20836; 1.
DR Pfam; PF05173; DapB_C; 1.
DR Pfam; PF01113; DapB_N; 1.
DR PIRSF; PIRSF000161; DHPR; 1.
DR SUPFAM; SSF51735; SSF51735; 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; Reference proteome.
FT CHAIN 1..216
FT /note="4-hydroxy-tetrahydrodipicolinate reductase"
FT /id="PRO_0000141502"
FT ACT_SITE 127
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00102"
FT ACT_SITE 131
FT /note="Proton donor"
FT /evidence="ECO:0000305"
FT BINDING 9..12
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:18250105,
FT ECO:0007744|PDB:1VM6"
FT BINDING 71..73
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:18250105,
FT ECO:0007744|PDB:1VM6"
FT BINDING 95..98
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:18250105,
FT ECO:0007744|PDB:1VM6"
FT BINDING 128
FT /ligand="(S)-2,3,4,5-tetrahydrodipicolinate"
FT /ligand_id="ChEBI:CHEBI:16845"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00102"
FT BINDING 131
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000269|PubMed:18250105,
FT ECO:0007744|PDB:1VM6"
FT BINDING 137..138
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..6
FT /evidence="ECO:0007829|PDB:1VM6"
FT TURN 7..9
FT /evidence="ECO:0007829|PDB:1VM6"
FT HELIX 11..22
FT /evidence="ECO:0007829|PDB:1VM6"
FT STRAND 26..32
FT /evidence="ECO:0007829|PDB:1VM6"
FT STRAND 35..38
FT /evidence="ECO:0007829|PDB:1VM6"
FT STRAND 43..47
FT /evidence="ECO:0007829|PDB:1VM6"
FT HELIX 51..53
FT /evidence="ECO:0007829|PDB:1VM6"
FT HELIX 54..64
FT /evidence="ECO:0007829|PDB:1VM6"
FT STRAND 67..70
FT /evidence="ECO:0007829|PDB:1VM6"
FT HELIX 77..86
FT /evidence="ECO:0007829|PDB:1VM6"
FT TURN 87..89
FT /evidence="ECO:0007829|PDB:1VM6"
FT STRAND 90..94
FT /evidence="ECO:0007829|PDB:1VM6"
FT HELIX 100..115
FT /evidence="ECO:0007829|PDB:1VM6"
FT TURN 116..118
FT /evidence="ECO:0007829|PDB:1VM6"
FT STRAND 119..127
FT /evidence="ECO:0007829|PDB:1VM6"
FT HELIX 137..145
FT /evidence="ECO:0007829|PDB:1VM6"
FT STRAND 152..156
FT /evidence="ECO:0007829|PDB:1VM6"
FT STRAND 163..169
FT /evidence="ECO:0007829|PDB:1VM6"
FT STRAND 171..181
FT /evidence="ECO:0007829|PDB:1VM6"
FT HELIX 185..198
FT /evidence="ECO:0007829|PDB:1VM6"
FT STRAND 203..206
FT /evidence="ECO:0007829|PDB:1VM6"
FT HELIX 208..212
FT /evidence="ECO:0007829|PDB:1VM6"
SQ SEQUENCE 216 AA; 23731 MW; 2C5670DF62C85528 CRC64;
MKYGIVGYSG RMGQEIQKVF SEKGHELVLK VDVNGVEELD SPDVVIDFSS PEALPKTVDL
CKKYRAGLVL GTTALKEEHL QMLRELSKEV PVVQAYNFSI GINVLKRFLS ELVKVLEDWD
VEIVETHHRF KKDAPSGTAI LLESALGKSV PIHSLRVGGV PGDHVVVFGN IGETIEIKHR
AISRTVFAIG ALKAAEFLVG KDPGMYSFEE VIFGGE
