Rule : Erythronate-4-phosphate dehydrogenase (PDXB)

Rule Description

NRULE_0209

Rule name

PDXB

Created

2013-05-09

Protein name

Full: Erythronate-4-phosphate dehydrogenase
EC: EC 1.1.1.290

Gene name

pdxB

Rule Trigger

HAMAP; MF_01825; hit=1

Cross Reference

Gene Ontology

GO: GO:0005737, C:cytoplasm, IEA:UniProtKB-SubCell; GO:0033711, F:4-phosphoerythronate dehydrogenase activity, IDA:EcoCyc; GO:0051287, F:NAD binding, IDA:EcoCyc; GO:0042823, P:pyridoxal phosphate biosynthetic process, IDA:EcoCyc; GO:0008615, P:pyridoxine biosynthetic process, IDA:EcoCyc

Phylogenomic databases

eggNOG: COG0111, -
HOGENOM: HOG000234432, -
KO: K03473, -
ProtClustDB: PRK15438, -

Enzyme and pathway databases

BioCyc: MetaCyc:ERYTHRON4PDEHYDROG-MONOMER, -
BRENDA: 1.1.1.290, 2026
UniPathway: UPA00244, UER00310

Family and domain databases

HAMAP: MF_01825, PdxB, 1, -
InterPro: IPR006139, D-isomer_2_OHA_DH_cat_dom; IPR006140, D-isomer_2_OHA_DH_NAD-bd; IPR020921, Erythronate-4-P_DHase; IPR024531, Erythronate-4-P_DHase_dimer
Pfam: PF00389, 2-Hacid_dh, 1; PF02826, 2-Hacid_dh_C, 1; PF11890, DUF3410, 1
PROSITE: PS00065, D_2_HYDROXYACID_DH_1, 1; PS00670, D_2_HYDROXYACID_DH_2, FALSE_NEG; PS00671, D_2_HYDROXYACID_DH_3, 1

Feature

P05459 Escherichia coli (strain K12).

ACT_SITE	208	By similarity.
ACT_SITE	237	By similarity.
ACT_SITE	254	Proton donor (By similarity).
BINDING	45	Substrate (By similarity).
BINDING	66	Substrate (By similarity).
BINDING	146	NAD (By similarity).
BINDING	175	NAD; via carbonyl oxygen (By similarity).
BINDING	232	NAD (By similarity).
BINDING	257	NAD; via amide nitrogen (By similarity).
BINDING	258	Substrate (By similarity).

General annotation

Function: Catalyzes the oxidation of erythronate-4-phosphate to 3- hydroxy-2-oxo-4-phosphonooxybutanoate (By similarity)
Catalytic activity: 4-phospho-D-erythronate + NAD(+) = (3R)-3- hydroxy-2-oxo-4-phosphonooxybutanoate + NADH
Pathway: Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4- phosphate: step 2/5
Subunit structure: Homodimer (By similarity)
Subcellular location: Cytoplasm (Potential)
Sequence similarities: Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. PdxB subfamily

Reference

P05459 Escherichia coli (strain K12).

2681152: Divergent transcription of pdxB and homology between the pdxB and serA gene products in Escherichia coli K-12. (J Bacteriol. 1989)
9205837: Construction of a contiguous 874-kb sequence of the Escherichia coli -K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features. (DNA Res. 1997)
9278503: The complete genome sequence of Escherichia coli K-12. (Science. 1997)
16738553: Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. (Mol Syst Biol. 2006)
2991861: Structural features of the hisT operon of Escherichia coli K-12. (Nucleic Acids Res. 1985)
3029016: Structural analysis of the Escherichia coli K-12 hisT operon by using a kanamycin resistance cassette. (J Bacteriol. 1987)
8595869: 4-Phospho-hydroxy-L-threonine is an obligatory intermediate in pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12. (FEMS Microbiol Lett. 1996)
9696782: Involvement of the gapA- and epd (gapB)-encoded dehydrogenases in pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12. (J Bacteriol. 1998)

Related Function

Function name
Vitamin B6 biosynthesis (PdxA/PdxJ pathway)

CDS


Scientific name	NBRC No.	CDS	Product name
Acinetobacter radioresistens	102413	ACRAD_02_01070	erythronate-4-phosphate dehydrogenase
Acinetobacter sp.	100985	ACT4_023_01680	erythronate-4-phosphate dehydrogenase
Alteromonas macleodii	102226	MASE_11690	erythronate-4-phosphate dehydrogenase
Bacteroides vulgatus	14291	BVU_1060	erythronate-4-phosphate dehydrogenase
Chitinispirillum alkaliphilum		CHISP_0661	Erythronate-4-phosphate dehydrogenase
Chitinivibrio alkaliphilus		CALK_0890	erythronate-4-phosphate dehydrogenase
Edwardsiella tarda	105688	ET1_09_00070	erythronate-4-phosphate dehydrogenase
Enterobacter aerogenes	13534	EAE_24600	erythronate-4-phosphate dehydrogenase PdxB
Enterobacter cloacae subsp. cloacae	13535	ECL_03669	erythronate-4-phosphate dehydrogenase
Enterobacter hormaechei	105718	HMPREF9086_3236	4-phosphoerythronate dehydrogenase
Escherichia coli	3972	EcolC_1332	D-isomer specific 2-hydroxyacid dehydrogenase catalytic region
Escherichia coli	13500	WFL_12285	erythronate-4-phosphate dehydrogenase PdxB
Escherichia coli	12713	Y75_2326	erythronate-4-phosphate dehydrogenase
Escherichia fergusonii	102419	EFER_0843	erythronate-4-phosphate dehydrogenase
Escherichia hermannii	105704	EH105704_01_07640	erythronate-4-phosphate dehydrogenase
Halomonas elongata	15536	HELO_2011	erythronate-4-phosphate dehydrogenase
Ignavibacterium album	101810	IALB_2961	Erythronate-4-phosphate dehydrogenase
Klebsiella pneumoniae	14438	KPR_1996
Klebsiella pneumoniae subsp. rhinoscleromatis	105682	HMPREF0484_3513	4-phosphoerythronate dehydrogenase
Lentisphaera araneosa		LNTAR_23439	erythronate-4-phosphate dehydrogenase
Marinomonas mediterranea	103028	Marme_2180	Erythronate-4-phosphate dehydrogenase
Mariprofundus ferrooxydans		SPV1_08988	erythronate-4-phosphate dehydrogenase
Photobacterium damselae subsp. damselae corrig.	15633	VDA_001532	erythronate-4-phosphate dehydrogenase
Proteus mirabilis	105697	HMPREF0693_1434	4-phosphoerythronate dehydrogenase
Providencia alcalifaciens	105687	PROVALCAL_03334	4-phosphoerythronate dehydrogenase
Pseudomonas putida	100650	PP_2117	erythronate-4-phosphate dehydrogenase
Pseudomonas stutzeri	14165	PSTAB_1716	erythronate-4-phosphate dehydrogenase
Rahnella aquatilis	105701	Rahaq2_1300	phosphoglycerate dehydrogenase-like oxidoreductase
Salinibacter ruber		SRU_2082	erythronate-4-phosphate dehydrogenase
Serratia odorifera	102598	HMPREF0758_2754	4-phosphoerythronate dehydrogenase
Shimwellia blattae	105725	EB105725_04_00250	erythronate-4-phosphate dehydrogenase
Vibrio alginolyticus	15630	N646_1296	erythronate-4-phosphate dehydrogenase
Vibrio ichthyoenteri	15847	VII00023_13402	erythronate-4-phosphate dehydrogenase
Vibrio metschnikovii	103153	VIB_000791	erythronate-4-phosphate dehydrogenase
Vibrio orientalis	15638	VIOR3934_10145	erythronate-4-phosphate dehydrogenase
Vibrio tubiashii	15644	VITU9109_12633	erythronate-4-phosphate dehydrogenase
Vibrio vulnificus	15645	B736_04415	erythronate-4-phosphate dehydrogenase
Yersinia bercovieri	105717	yberc0001_27410	Erythronate-4-phosphate dehydrogenase
Yersinia rohdei	105715	yrohd0001_24920	Erythronate-4-phosphate dehydrogenase