Q87MN8 (PDXB_VIBPA) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Erythronate-4-phosphate dehydrogenase
EC=1.1.1.290

Gene names

Name:	pdxB
Ordered Locus Names:	VP2193

Organism

Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633) [Complete proteome] [HAMAP]

Taxonomic identifier

223926 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio › Vibrio harveyi group › Vibrio parahaemolyticus

Protein attributes

Sequence length	377 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Catalyzes the oxidation of erythronate-4-phosphate to 3-hydroxy-2-oxo-4-phosphonooxybutanoate By similarity. HAMAP-Rule MF_01825
Catalytic activity	4-phospho-D-erythronate + NAD+ = (3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + NADH. HAMAP-Rule MF_01825
Pathway	Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 2/5. HAMAP-Rule MF_01825
Subunit structure	Homodimer By similarity.
Subcellular location	Cytoplasm Potential HAMAP-Rule MF_01825.
Sequence similarities	Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. PdxB subfamily.

Ontologies

Keywords
Biological process	Pyridoxine biosynthesis
Cellular component	Cytoplasm
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	pyridoxine biosynthetic process Inferred from electronic annotation. Source: HAMAP
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	4-phosphoerythronate dehydrogenase activity Inferred from electronic annotation. Source: EC NAD binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 377	377	Erythronate-4-phosphate dehydrogenase HAMAP-Rule MF_01825		PRO_0000075992
Regions
	Nucleotide binding	127 – 128	2	NAD By similarity
Sites
	Active site	209	1	By similarity
	Active site	238	1	By similarity
	Active site	255	1	Proton donor By similarity
	Binding site	45	1	Substrate By similarity
	Binding site	67	1	Substrate By similarity
	Binding site	147	1	NAD By similarity
	Binding site	176	1	NAD; via carbonyl oxygen By similarity
	Binding site	233	1	NAD By similarity
	Binding site	258	1	NAD; via amide nitrogen By similarity
	Binding site	259	1	Substrate By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q87MN8 [UniParc]. Last modified June 1, 2003. Version 1. Checksum: 4648285895FC9DF6	FASTA	377	41,658
	10 20 30 40 50 60 MKIIVDENMP YAEELFSQLG EVILKPGRTL TADDLIDIDA LMIRSVTKVN AELISKANKL 70 80 90 100 110 120 KFVGTATAGM DHVDQALLKE KGIFFTAAPG CNKVGVAEYA FSVMMVLAQQ QGFSVFDKTV 130 140 150 160 170 180 GIIGAGQVGS YLEKCLKGMG INVLINDPFK QEAGDPRSFT PLAELIEQSD IITLHTPITK 190 200 210 220 230 240 DGLHPTHHLI DEKVLNGLRG DQILINAARG PVVDNQALKQ RLMKQDGFTA ALDVFEFEPE 250 260 270 280 290 300 VDMELLPLLA FATPHVAGYG LEGKARGTTM IFNSYCEFLN NELRAHASDL LPTAPVPTMM 310 320 330 340 350 360 LDRAWDEATL HNITQLIYDV RKDDALFRRE ISKPGAFDLM RKNYWDRREY SAVTLVGNET 370 CNLAPLAELG FQIEVSQ

References

[1]

"Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism distinct from that of V. cholerae." Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K., Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S., Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T. Lancet 361:743-749(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: RIMD 2210633.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BA000031 Genomic DNA. Translation: BAC60456.1.
RefSeq	NP_798572.1. NC_004603.1.
3D structure databases
ProteinModelPortal	Q87MN8.
ModBase	Search...
Protein-protein interaction databases
STRING	223926.VP2193.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	BAC60456; BAC60456; BAC60456.
GeneID	1189706.
KEGG	vpa:VP2193.
PATRIC	20142536. VBIVibPar50997_2097.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0111.
HOGENOM	HOG000234432.
KO	K03473.
OMA	SSAPGCN.
ProtClustDB	CLSK874680.
Enzyme and pathway databases
UniPathway	UPA00244; UER00310.
Family and domain databases
Gene3D	3.40.50.720. 2 hits.
HAMAP	MF_01825. PdxB.
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. IPR016040. NAD(P)-bd_dom. [Graphical view]
PANTHER	PTHR10996:SF4. PTHR10996:SF4. 1 hit.
Pfam	PF00389. 2-Hacid_dh. 1 hit. PF02826. 2-Hacid_dh_C. 1 hit. PF11890. DUF3410. 1 hit. [Graphical view]
PROSITE	PS00065. D_2_HYDROXYACID_DH_1. False negative. PS00670. D_2_HYDROXYACID_DH_2. False negative. PS00671. D_2_HYDROXYACID_DH_3. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PDXB_VIBPA

Accession

Primary (citable) accession number: Q87MN8

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 13, 2004
Last sequence update:	June 1, 2003
Last modified:	May 1, 2013
This is version 69 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program