PDXB_PSEAE
ID PDXB_PSEAE Reviewed; 380 AA.
AC Q9I3W9;
DT 13-APR-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 128.
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=PA1375;
OS Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM
OS 14847 / LMG 12228 / 1C / PRS 101 / PAO1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=208964;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=10984043; DOI=10.1038/35023079;
RA Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
RA Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
RA Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
RA Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
RA Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T., Reizer J.,
RA Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
RT "Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic
RT pathogen.";
RL Nature 406:959-964(2000).
RN [2]
RP CRYSTALLIZATION, AND SUBUNIT.
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=16511285; DOI=10.1107/s1744309106000649;
RA Ha J.Y., Lee J.H., Kim K.H., Kim D.J., Lee H.H., Kim H.-K., Yoon H.-J.,
RA Suh S.W.;
RT "Overexpression, crystallization and preliminary X-ray crystallographic
RT analysis of erythronate-4-phosphate dehydrogenase from Pseudomonas
RT aeruginosa.";
RL Acta Crystallogr. F 62:139-141(2006).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH NAD AND PHOSPHATE OR
RP SUBSTRATE ANALOG, SUBUNIT, CATALYTIC MECHANISM, DOMAIN, ACTIVE SITE, AND
RP DISULFIDE BOND.
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=17217963; DOI=10.1016/j.jmb.2006.12.038;
RA Ha J.Y., Lee J.H., Kim K.H., Kim D.J., Lee H.H., Kim H.-K., Yoon H.-J.,
RA Suh S.W.;
RT "Crystal structure of D-erythronate-4-phosphate dehydrogenase complexed
RT with NAD.";
RL J. Mol. Biol. 366:1294-1304(2007).
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 ECO:0000269|PubMed:16511285, ECO:0000269|PubMed:17217963}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01825}.
CC -!- DOMAIN: Each subunit can be divided into three discernible structural
CC domains: the lid domain, the nucleotide-binding domain, and the C-
CC terminal dimerization domain. PdxB has a unique dimeric structure among
CC NAD-dependent D-isomer specific 2-hydroxyacid dehydrogenases due to the
CC presence of its dimerization domain at its C-terminus.
CC {ECO:0000305|PubMed:17217963}.
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; AE004091; AAG04764.1; -; Genomic_DNA.
DR PIR; C83473; C83473.
DR RefSeq; NP_250066.1; NC_002516.2.
DR RefSeq; WP_003112396.1; NZ_QZGE01000005.1.
DR PDB; 2O4C; X-ray; 2.30 A; A/B=1-380.
DR PDBsum; 2O4C; -.
DR AlphaFoldDB; Q9I3W9; -.
DR SMR; Q9I3W9; -.
DR STRING; 287.DR97_423; -.
DR PaxDb; Q9I3W9; -.
DR PRIDE; Q9I3W9; -.
DR EnsemblBacteria; AAG04764; AAG04764; PA1375.
DR GeneID; 881132; -.
DR KEGG; pae:PA1375; -.
DR PATRIC; fig|208964.12.peg.1427; -.
DR PseudoCAP; PA1375; -.
DR HOGENOM; CLU_019796_4_0_6; -.
DR InParanoid; Q9I3W9; -.
DR OMA; SAPGCNA; -.
DR PhylomeDB; Q9I3W9; -.
DR BioCyc; PAER208964:G1FZ6-1401-MON; -.
DR BRENDA; 1.1.1.290; 5087.
DR UniPathway; UPA00244; UER00310.
DR EvolutionaryTrace; Q9I3W9; -.
DR Proteomes; UP000002438; 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; 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; PS00671; D_2_HYDROXYACID_DH_3; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Disulfide bond; NAD; Oxidoreductase;
KW Pyridoxine biosynthesis; Reference proteome.
FT CHAIN 1..380
FT /note="Erythronate-4-phosphate dehydrogenase"
FT /id="PRO_0000075982"
FT ACT_SITE 208
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825,
FT ECO:0000305|PubMed:17217963"
FT ACT_SITE 237
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825,
FT ECO:0000305|PubMed:17217963"
FT ACT_SITE 254
FT /note="Proton donor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825,
FT ECO:0000305|PubMed:17217963"
FT BINDING 45
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825,
FT ECO:0000305|PubMed:17217963"
FT BINDING 66
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825,
FT ECO:0000305|PubMed:17217963"
FT BINDING 126..127
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825,
FT ECO:0000269|PubMed:17217963"
FT BINDING 146
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825,
FT ECO:0000269|PubMed:17217963"
FT BINDING 175
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825,
FT ECO:0000269|PubMed:17217963"
FT BINDING 206..208
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825,
FT ECO:0000269|PubMed:17217963"
FT BINDING 232
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825,
FT ECO:0000269|PubMed:17217963"
FT BINDING 257
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825,
FT ECO:0000269|PubMed:17217963"
FT BINDING 258
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825,
FT ECO:0000305|PubMed:17217963"
FT DISULFID 65..90
FT /evidence="ECO:0000269|PubMed:17217963"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 12..16
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 17..19
FT /evidence="ECO:0007829|PDB:2O4C"
FT STRAND 20..25
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 27..29
FT /evidence="ECO:0007829|PDB:2O4C"
FT TURN 32..37
FT /evidence="ECO:0007829|PDB:2O4C"
FT STRAND 39..43
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 51..54
FT /evidence="ECO:0007829|PDB:2O4C"
FT STRAND 61..64
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 74..80
FT /evidence="ECO:0007829|PDB:2O4C"
FT STRAND 83..85
FT /evidence="ECO:0007829|PDB:2O4C"
FT TURN 88..91
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 92..110
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 114..116
FT /evidence="ECO:0007829|PDB:2O4C"
FT STRAND 118..122
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 126..137
FT /evidence="ECO:0007829|PDB:2O4C"
FT STRAND 141..145
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 147..152
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 161..167
FT /evidence="ECO:0007829|PDB:2O4C"
FT STRAND 169..173
FT /evidence="ECO:0007829|PDB:2O4C"
FT STRAND 179..183
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 191..195
FT /evidence="ECO:0007829|PDB:2O4C"
FT STRAND 201..205
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 209..211
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 214..222
FT /evidence="ECO:0007829|PDB:2O4C"
FT STRAND 227..232
FT /evidence="ECO:0007829|PDB:2O4C"
FT TURN 235..238
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 242..245
FT /evidence="ECO:0007829|PDB:2O4C"
FT STRAND 249..251
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 260..278
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 286..288
FT /evidence="ECO:0007829|PDB:2O4C"
FT STRAND 294..300
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 306..317
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 321..329
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 335..347
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 355..357
FT /evidence="ECO:0007829|PDB:2O4C"
FT STRAND 359..361
FT /evidence="ECO:0007829|PDB:2O4C"
FT HELIX 366..375
FT /evidence="ECO:0007829|PDB:2O4C"
FT STRAND 378..380
FT /evidence="ECO:0007829|PDB:2O4C"
SQ SEQUENCE 380 AA; 41002 MW; 36F6B0F68909D05D CRC64;
MRILADENIP VVDAFFADQG SIRRLPGRAI DRAALAEVDV LLVRSVTEVS RAALAGSPVR
FVGTCTIGTD HLDLDYFAEA GIAWSSAPGC NARGVVDYVL GCLLAMAEVR GADLAERTYG
VVGAGQVGGR LVEVLRGLGW KVLVCDPPRQ AREPDGEFVS LERLLAEADV ISLHTPLNRD
GEHPTRHLLD EPRLAALRPG TWLVNASRGA VVDNQALRRL LEGGADLEVA LDVWEGEPQA
DPELAARCLI ATPHIAGYSL EGKLRGTAQI YQAYCAWRGI AERVSLQDVL PETWLAGLQL
NPGCDPAWAL ATLCRAVYDP RSDDAAFRRS LTGDSATRRA AFDALRKHYP PRREITGLRV
ATGGQAELQR VVRALGAQLV
