ID A0A2D0KWL3_9GAMM Unreviewed; 375 AA.
AC A0A2D0KWL3;
DT 20-DEC-2017, integrated into UniProtKB/TrEMBL.
DT 20-DEC-2017, sequence version 1.
DT 27-MAR-2024, entry version 32.
DE RecName: Full=Erythronate-4-phosphate dehydrogenase {ECO:0000256|HAMAP-Rule:MF_01825};
DE EC=1.1.1.290 {ECO:0000256|HAMAP-Rule:MF_01825};
GN Name=pdxB {ECO:0000256|HAMAP-Rule:MF_01825};
GN ORFNames=Xsto_00116 {ECO:0000313|EMBL:PHM67826.1};
OS Xenorhabdus stockiae.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Morganellaceae; Xenorhabdus.
OX NCBI_TaxID=351614 {ECO:0000313|EMBL:PHM67826.1, ECO:0000313|Proteomes:UP000222366};
RN [1] {ECO:0000313|EMBL:PHM67826.1, ECO:0000313|Proteomes:UP000222366}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 17904 {ECO:0000313|EMBL:PHM67826.1,
RC ECO:0000313|Proteomes:UP000222366};
RX PubMed=28993611; DOI=10.1038/s41564-017-0039-9;
RA Tobias N.J., Wolff H., Djahanschiri B., Grundmann F., Kronenwerth M.,
RA Shi Y.M., Simonyi S., Grun P., Shapiro-Ilan D., Pidot S.J., Stinear T.P.,
RA Ebersberger I., Bode H.B.;
RT "Natural product diversity associated with the nematode symbionts
RT Photorhabdus and Xenorhabdus.";
RL Nat. Microbiol. 2:1676-1685(2017).
CC -!- FUNCTION: Catalyzes the oxidation of erythronate-4-phosphate to 3-
CC hydroxy-2-oxo-4-phosphonooxybutanoate. {ECO:0000256|HAMAP-
CC Rule:MF_01825}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-phospho-D-erythronate + NAD(+) = (R)-3-hydroxy-2-oxo-4-
CC phosphooxybutanoate + H(+) + NADH; Xref=Rhea:RHEA:18829,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945,
CC ChEBI:CHEBI:58538, ChEBI:CHEBI:58766; EC=1.1.1.290;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01825};
CC -!- PATHWAY: Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis;
CC pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 2/5.
CC {ECO:0000256|HAMAP-Rule:MF_01825}.
CC -!- SUBUNIT: Homodimer. {ECO:0000256|HAMAP-Rule:MF_01825}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01825}.
CC -!- SIMILARITY: Belongs to the D-isomer specific 2-hydroxyacid
CC dehydrogenase family. PdxB subfamily. {ECO:0000256|HAMAP-
CC Rule:MF_01825}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_01825}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:PHM67826.1}.
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DR EMBL; NJAJ01000001; PHM67826.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A2D0KWL3; -.
DR UniPathway; UPA00244; UER00310.
DR Proteomes; UP000222366; Unassembled WGS sequence.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0033711; F:4-phosphoerythronate dehydrogenase activity; IEA:UniProtKB-EC.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0046983; F:protein dimerization activity; IEA:InterPro.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IEA:UniProtKB-UniRule.
DR CDD; cd12158; ErythrP_dh; 1.
DR Gene3D; 3.30.1370.170; -; 1.
DR Gene3D; 3.40.50.720; NAD(P)-binding Rossmann-like Domain; 2.
DR HAMAP; MF_01825; PdxB; 1.
DR InterPro; IPR006139; D-isomer_2_OHA_DH_cat_dom.
DR InterPro; IPR029753; D-isomer_DH_CS.
DR InterPro; IPR029752; D-isomer_DH_CS1.
DR InterPro; IPR006140; D-isomer_DH_NAD-bd.
DR InterPro; IPR020921; Erythronate-4-P_DHase.
DR InterPro; IPR024531; Erythronate-4-P_DHase_dimer.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR InterPro; IPR038251; PdxB_dimer_sf.
DR PANTHER; PTHR42938:SF40; ERYTHRONATE-4-PHOSPHATE DEHYDROGENASE; 1.
DR PANTHER; PTHR42938; FORMATE DEHYDROGENASE 1; 1.
DR Pfam; PF00389; 2-Hacid_dh; 1.
DR Pfam; PF02826; 2-Hacid_dh_C; 1.
DR Pfam; PF11890; DUF3410; 1.
DR SUPFAM; SSF52283; Formate/glycerate dehydrogenase catalytic domain-like; 1.
DR SUPFAM; SSF51735; NAD(P)-binding Rossmann-fold domains; 1.
DR PROSITE; PS00065; D_2_HYDROXYACID_DH_1; 1.
DR PROSITE; PS00671; D_2_HYDROXYACID_DH_3; 1.
PE 3: Inferred from homology;
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_01825};
KW NAD {ECO:0000256|ARBA:ARBA00023027, ECO:0000256|HAMAP-Rule:MF_01825};
KW Oxidoreductase {ECO:0000256|ARBA:ARBA00023002, ECO:0000256|HAMAP-
KW Rule:MF_01825};
KW Pyridoxine biosynthesis {ECO:0000256|ARBA:ARBA00023096, ECO:0000256|HAMAP-
KW Rule:MF_01825}.
FT DOMAIN 5..280
FT /note="D-isomer specific 2-hydroxyacid dehydrogenase
FT catalytic"
FT /evidence="ECO:0000259|Pfam:PF00389"
FT DOMAIN 111..256
FT /note="D-isomer specific 2-hydroxyacid dehydrogenase NAD-
FT binding"
FT /evidence="ECO:0000259|Pfam:PF02826"
FT DOMAIN 289..369
FT /note="Erythronate-4-phosphate dehydrogenase dimerisation"
FT /evidence="ECO:0000259|Pfam:PF11890"
FT ACT_SITE 208
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01825"
FT ACT_SITE 237
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01825"
FT ACT_SITE 254
FT /note="Proton donor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01825"
FT BINDING 45
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01825"
FT BINDING 66
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01825"
FT BINDING 146
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01825"
FT BINDING 175
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01825"
FT BINDING 206..208
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01825"
FT BINDING 232
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01825"
FT BINDING 257
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01825"
FT BINDING 258
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01825"
SQ SEQUENCE 375 AA; 41053 MW; B1126F5C39AE7C76 CRC64;
MKILVDENMP YAEQLFKQLG EVQAIPGRPV PEGVLEHADA FMVRSVTKVS ESLLKGSAVK
FVGTATAGMD HVDQPWLEQA GIGFSAAPGC NAIAVVEYVF SALMILAEQD QFQLKDKTVG
IVGVGNVGGR LAARLAALGV KTLLCDPPRA DRGDEGEFWP LEKLVKEADI LTFHTPLNTS
GPYQTYHLAD AELLSALPDN RILINASRGE VVDNQALLSA LQNGKKLRVV LDVWEPEPNL
SLPLLERVDI GTPHIAGYTL EGKARGTTQV FEAYCEFLGK PQKTALSDLL PESDFSHITV
RGEVTQSILK RLMHLVYDVR RDDAPLRQVA GQNGAFDQLR KNYPERREWS SLTVHCDSES
SAQLLSQIGF DAKVI
//