PDXB_VIBCH
ID PDXB_VIBCH Reviewed; 381 AA.
AC Q9KQ92;
DT 13-APR-2004, integrated into UniProtKB/Swiss-Prot.
DT 13-APR-2004, sequence version 2.
DT 03-AUG-2022, entry version 126.
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=VC_2108;
OS Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=243277;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 39315 / El Tor Inaba N16961;
RX PubMed=10952301; DOI=10.1038/35020000;
RA Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L.,
RA Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R.,
RA Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D.,
RA Vamathevan J.J., Bass S., Qin H., Dragoi I., Sellers P., McDonald L.A.,
RA Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L.,
RA Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.;
RT "DNA sequence of both chromosomes of the cholera pathogen Vibrio
RT cholerae.";
RL Nature 406:477-483(2000).
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF95254.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AE003852; AAF95254.1; ALT_INIT; Genomic_DNA.
DR PIR; C82118; C82118.
DR RefSeq; NP_231740.1; NC_002505.1.
DR RefSeq; WP_000697483.1; NZ_LT906614.1.
DR PDB; 5DT9; X-ray; 2.66 A; A=1-381.
DR PDBsum; 5DT9; -.
DR AlphaFoldDB; Q9KQ92; -.
DR SMR; Q9KQ92; -.
DR STRING; 243277.VC_2108; -.
DR DNASU; 2613364; -.
DR EnsemblBacteria; AAF95254; AAF95254; VC_2108.
DR KEGG; vch:VC_2108; -.
DR PATRIC; fig|243277.26.peg.2014; -.
DR eggNOG; COG0111; Bacteria.
DR HOGENOM; CLU_019796_4_0_6; -.
DR OMA; SAPGCNA; -.
DR UniPathway; UPA00244; UER00310.
DR Proteomes; UP000000584; Chromosome 1.
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; NAD; Oxidoreductase; Pyridoxine biosynthesis;
KW Reference proteome.
FT CHAIN 1..381
FT /note="Erythronate-4-phosphate dehydrogenase"
FT /id="PRO_0000075991"
FT ACT_SITE 209
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT ACT_SITE 238
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT ACT_SITE 255
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 67
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 127..128
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 147
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 176
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 233
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 258
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT BINDING 259
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01825"
FT STRAND 1..6
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 12..16
FT /evidence="ECO:0007829|PDB:5DT9"
FT TURN 17..19
FT /evidence="ECO:0007829|PDB:5DT9"
FT STRAND 20..25
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 27..29
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 32..35
FT /evidence="ECO:0007829|PDB:5DT9"
FT STRAND 39..43
FT /evidence="ECO:0007829|PDB:5DT9"
FT STRAND 45..47
FT /evidence="ECO:0007829|PDB:5DT9"
FT TURN 51..56
FT /evidence="ECO:0007829|PDB:5DT9"
FT STRAND 62..68
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 75..80
FT /evidence="ECO:0007829|PDB:5DT9"
FT STRAND 84..86
FT /evidence="ECO:0007829|PDB:5DT9"
FT TURN 89..92
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 93..111
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 115..117
FT /evidence="ECO:0007829|PDB:5DT9"
FT STRAND 120..123
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 127..138
FT /evidence="ECO:0007829|PDB:5DT9"
FT STRAND 143..146
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 148..153
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 162..168
FT /evidence="ECO:0007829|PDB:5DT9"
FT STRAND 170..174
FT /evidence="ECO:0007829|PDB:5DT9"
FT STRAND 180..184
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 192..195
FT /evidence="ECO:0007829|PDB:5DT9"
FT STRAND 203..206
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 210..212
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 215..222
FT /evidence="ECO:0007829|PDB:5DT9"
FT STRAND 229..234
FT /evidence="ECO:0007829|PDB:5DT9"
FT TURN 243..245
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 246..248
FT /evidence="ECO:0007829|PDB:5DT9"
FT STRAND 249..252
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 261..279
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 287..290
FT /evidence="ECO:0007829|PDB:5DT9"
FT STRAND 298..300
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 307..317
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 320..330
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 336..342
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 350..352
FT /evidence="ECO:0007829|PDB:5DT9"
FT STRAND 353..357
FT /evidence="ECO:0007829|PDB:5DT9"
FT HELIX 364..369
FT /evidence="ECO:0007829|PDB:5DT9"
FT STRAND 372..375
FT /evidence="ECO:0007829|PDB:5DT9"
SQ SEQUENCE 381 AA; 41865 MW; CC900794B7B81360 CRC64;
MKILIDENMP YAQALFSQLG EVILKPGRTL TADDLIDVDA LMIRSVTKVN DALLAKANRL
KFVGTATAGM DHVDQALLRE RGIFFTAAPG CNKVGVAEYV FSVLMVLAQQ QGFSVFDKTV
GIIGAGQVGS YLAKCLSGIG MKVLLNDPPK QAQGDEREFT ELETLLKQAD VITLHTPITR
GGEWPTHHLI DAAILEQLRS DQILINAARG PVVDNAALKA RLQQGDGFTA VLDVFEFEPQ
VDMELLPLLA FATPHIAGYG LEGKARGTTM IFNSYCEFLG SAHCANPASL LPKAPVPKVY
LERAWDEETL RTLTQIIYDV RKDDAQFRRE IHQPGAFDLM RKHYWDRREY SAVTLAGGAD
CHLAPLAKLG FQVEVCDEPT I
