PDXB_SALTY
ID PDXB_SALTY Reviewed; 378 AA.
AC P60802; Q8XGK3;
DT 13-APR-2004, integrated into UniProtKB/Swiss-Prot.
DT 13-APR-2004, sequence version 1.
DT 03-AUG-2022, entry version 108.
DE RecName: Full=Erythronate-4-phosphate dehydrogenase {ECO:0000255|HAMAP-Rule:MF_01825};
DE EC=1.1.1.290 {ECO:0000255|HAMAP-Rule:MF_01825};
GN Name=pdxB {ECO:0000255|HAMAP-Rule:MF_01825}; OrderedLocusNames=STM2370;
OS Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Salmonella.
OX NCBI_TaxID=99287;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX PubMed=11677609; DOI=10.1038/35101614;
RA McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA Wilson R.K.;
RT "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL Nature 413:852-856(2001).
CC -!- FUNCTION: Catalyzes the oxidation of erythronate-4-phosphate to 3-
CC hydroxy-2-oxo-4-phosphonooxybutanoate. {ECO:0000255|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:0000255|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:0000255|HAMAP-Rule:MF_01825}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01825}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01825}.
CC -!- SIMILARITY: Belongs to the D-isomer specific 2-hydroxyacid
CC dehydrogenase family. PdxB subfamily. {ECO:0000255|HAMAP-
CC Rule:MF_01825}.
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DR EMBL; AE006468; AAL21271.1; -; Genomic_DNA.
DR RefSeq; NP_461312.1; NC_003197.2.
DR RefSeq; WP_000699178.1; NC_003197.2.
DR PDB; 3OET; X-ray; 2.36 A; A/B/C/D/E/F/G/H=1-378.
DR PDBsum; 3OET; -.
DR AlphaFoldDB; P60802; -.
DR SMR; P60802; -.
DR STRING; 99287.STM2370; -.
DR PaxDb; P60802; -.
DR EnsemblBacteria; AAL21271; AAL21271; STM2370.
DR GeneID; 1253892; -.
DR KEGG; stm:STM2370; -.
DR PATRIC; fig|99287.12.peg.2509; -.
DR HOGENOM; CLU_019796_4_0_6; -.
DR OMA; SAPGCNA; -.
DR PhylomeDB; P60802; -.
DR BioCyc; SENT99287:STM2370-MON; -.
DR UniPathway; UPA00244; UER00310.
DR EvolutionaryTrace; P60802; -.
DR Proteomes; UP000001014; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0033711; F:4-phosphoerythronate dehydrogenase activity; IBA:GO_Central.
DR GO; GO:0051287; F:NAD binding; IEA:InterPro.
DR GO; GO:0046983; F:protein dimerization activity; IEA:InterPro.
DR GO; GO:0036001; P:'de novo' pyridoxal 5'-phosphate biosynthetic process; IBA:GO_Central.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IBA:GO_Central.
DR CDD; cd12158; ErythrP_dh; 1.
DR Gene3D; 3.30.1370.170; -; 1.
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 Pfam; PF00389; 2-Hacid_dh; 1.
DR Pfam; PF02826; 2-Hacid_dh_C; 1.
DR Pfam; PF11890; DUF3410; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR PROSITE; PS00065; D_2_HYDROXYACID_DH_1; 1.
DR PROSITE; PS00671; D_2_HYDROXYACID_DH_3; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; NAD; Oxidoreductase; Pyridoxine biosynthesis;
KW Reference proteome.
FT CHAIN 1..378
FT /note="Erythronate-4-phosphate dehydrogenase"
FT /id="PRO_0000075986"
FT ACT_SITE 208
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT ACT_SITE 237
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT ACT_SITE 254
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 45
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 66
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 146
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 175
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 232
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 257
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 258
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 12..16
FT /evidence="ECO:0007829|PDB:3OET"
FT STRAND 19..25
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 32..35
FT /evidence="ECO:0007829|PDB:3OET"
FT STRAND 39..43
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 51..54
FT /evidence="ECO:0007829|PDB:3OET"
FT STRAND 61..67
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 74..79
FT /evidence="ECO:0007829|PDB:3OET"
FT STRAND 83..85
FT /evidence="ECO:0007829|PDB:3OET"
FT TURN 88..91
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 92..109
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 114..116
FT /evidence="ECO:0007829|PDB:3OET"
FT STRAND 118..122
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 126..137
FT /evidence="ECO:0007829|PDB:3OET"
FT STRAND 141..145
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 147..151
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 161..167
FT /evidence="ECO:0007829|PDB:3OET"
FT STRAND 169..173
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 191..196
FT /evidence="ECO:0007829|PDB:3OET"
FT STRAND 201..205
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 209..211
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 214..222
FT /evidence="ECO:0007829|PDB:3OET"
FT STRAND 227..232
FT /evidence="ECO:0007829|PDB:3OET"
FT TURN 235..238
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 242..247
FT /evidence="ECO:0007829|PDB:3OET"
FT STRAND 248..251
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 260..277
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 286..289
FT /evidence="ECO:0007829|PDB:3OET"
FT STRAND 297..300
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 306..316
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 320..329
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 335..341
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 349..351
FT /evidence="ECO:0007829|PDB:3OET"
FT STRAND 352..358
FT /evidence="ECO:0007829|PDB:3OET"
FT HELIX 359..368
FT /evidence="ECO:0007829|PDB:3OET"
FT STRAND 371..374
FT /evidence="ECO:0007829|PDB:3OET"
SQ SEQUENCE 378 AA; 41298 MW; 365198C8CA796241 CRC64;
MKILVDENMP YARELFSRLG EVKAVPGRPI PVEELNHADA LMVRSVTKVN ESLLSGTPIN
FVGTATAGTD HVDEAWLKQA GIGFSAAPGC NAIAVVEYVF SALLMLAERD GFSLRDRTIG
IVGVGNVGSR LQTRLEALGI RTLLCDPPRA ARGDEGDFRT LDELVQEADV LTFHTPLYKD
GPYKTLHLAD ETLIRRLKPG AILINACRGP VVDNAALLAR LNAGQPLSVV LDVWEGEPDL
NVALLEAVDI GTSHIAGYTL EGKARGTTQV FEAYSAFIGR EQRVALETLL PAPEFGRITL
HGPLDQPTLK RLAHLVYDVR RDDAPLRKVA GIPGEFDKLR KNYLERREWS SLYVMCDDET
AAALLCKLGF NAVHHPAH
