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Protein

Erythronate-4-phosphate dehydrogenase

Gene

pdxB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Catalyzes the oxidation of erythronate-4-phosphate to 3-hydroxy-2-oxo-4-phosphonooxybutanoate.UniRule annotation

Catalytic activityi

4-phospho-D-erythronate + NAD+ = (3R)-3-hydroxy-2-oxo-4-phosphonooxybutanoate + NADH.UniRule annotation

Pathwayi: pyridoxine 5'-phosphate biosynthesis

This protein is involved in step 2 of the subpathway that synthesizes pyridoxine 5'-phosphate from D-erythrose 4-phosphate.UniRule annotation1 Publication
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. D-erythrose-4-phosphate dehydrogenase (epd)
  2. Erythronate-4-phosphate dehydrogenase (pdxB)
  3. Phosphoserine aminotransferase (serC)
  4. 4-hydroxythreonine-4-phosphate dehydrogenase (pdxA)
  5. Pyridoxine 5'-phosphate synthase (pdxJ)
This subpathway is part of the pathway pyridoxine 5'-phosphate biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxine 5'-phosphate from D-erythrose 4-phosphate, the pathway pyridoxine 5'-phosphate biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei45SubstrateUniRule annotation1
Binding sitei66SubstrateUniRule annotation1
Binding sitei146NADUniRule annotation1
Binding sitei175NAD; via carbonyl oxygenUniRule annotation1
Active sitei208UniRule annotation1
Binding sitei232NADUniRule annotation1
Active sitei237UniRule annotation1
Active sitei254Proton donorUniRule annotation1
Binding sitei257NAD; via amide nitrogenUniRule annotation1
Binding sitei258SubstrateUniRule annotation1

GO - Molecular functioni

  • 4-phosphoerythronate dehydrogenase activity Source: EcoCyc
  • NAD binding Source: EcoCyc

GO - Biological processi

  • pyridoxal phosphate biosynthetic process Source: EcoCyc
  • pyridoxine biosynthetic process Source: EcoCyc
  • serine family amino acid biosynthetic process Source: GO_Central
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Pyridoxine biosynthesis

Keywords - Ligandi

NAD

Enzyme and pathway databases

BioCyciEcoCyc:ERYTHRON4PDEHYDROG-MONOMER.
ECOL316407:JW2317-MONOMER.
MetaCyc:ERYTHRON4PDEHYDROG-MONOMER.
BRENDAi1.1.1.290. 2026.
UniPathwayiUPA00244; UER00310.

Names & Taxonomyi

Protein namesi
Recommended name:
Erythronate-4-phosphate dehydrogenaseUniRule annotation (EC:1.1.1.290UniRule annotation)
Gene namesi
Name:pdxBUniRule annotation
Ordered Locus Names:b2320, JW2317
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10692. pdxB.

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000759751 – 378Erythronate-4-phosphate dehydrogenaseAdd BLAST378

Proteomic databases

EPDiP05459.
PaxDbiP05459.
PRIDEiP05459.

Expressioni

Inductioni

During growth rate.1 Publication

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

BioGridi4259616. 19 interactors.
DIPiDIP-10449N.
IntActiP05459. 9 interactors.
STRINGi511145.b2320.

Structurei

3D structure databases

ProteinModelPortaliP05459.
SMRiP05459.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. PdxB subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CJ0. Bacteria.
COG0111. LUCA.
HOGENOMiHOG000234432.
InParanoidiP05459.
KOiK03473.
OMAiSAPGCNA.
PhylomeDBiP05459.

Family and domain databases

CDDicd12158. ErythrP_dh. 1 hit.
Gene3Di3.40.50.720. 2 hits.
HAMAPiMF_01825. PdxB. 1 hit.
InterProiIPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR029753. D-isomer_DH_CS.
IPR029752. D-isomer_DH_CS1.
IPR006140. D-isomer_DH_NAD-bd.
IPR020921. Erythronate-4-P_DHase.
IPR024531. Erythronate-4-P_DHase_dimer.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERiPTHR10996:SF111. PTHR10996:SF111. 1 hit.
PfamiPF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
PF11890. DUF3410. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
PROSITEiPS00065. D_2_HYDROXYACID_DH_1. 1 hit.
PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P05459-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKILVDENMP YARDLFSRLG EVTAVPGRPI PVAQLADADA LMVRSVTKVN
60 70 80 90 100
ESLLAGKPIK FVGTATAGTD HVDEAWLKQA GIGFSAAPGC NAIAVVEYVF
110 120 130 140 150
SSLLMLAERD GFSLYDRTVG IVGVGNVGRR LQARLEALGI KTLLCDPPRA
160 170 180 190 200
DRGDEGDFRS LDELVQRADI LTFHTPLFKD GPYKTLHLAD EKLIRSLKPG
210 220 230 240 250
AILINACRGA VVDNTALLTC LNEGQKLSVV LDVWEGEPEL NVELLKKVDI
260 270 280 290 300
GTSHIAGYTL EGKARGTTQV FEAYSKFIGH EQHVALDTLL PAPEFGRITL
310 320 330 340 350
HGPLDQPTLK RLVHLVYDVR RDDAPLRKVA GIPGEFDKLR KNYLERREWS
360 370
SLYVICDDAS AASLLCKLGF NAVHHPAR
Length:378
Mass (Da):41,368
Last modified:April 1, 1990 - v2
Checksum:i6CEF17691CF2C14A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M29962 Genomic DNA. Translation: AAA24308.1.
U76961 Genomic DNA. Translation: AAB36530.1.
U00096 Genomic DNA. Translation: AAC75380.1.
AP009048 Genomic DNA. Translation: BAA16177.1.
X02743 Genomic DNA. Translation: CAA26520.1.
M15541 Genomic DNA. Translation: AAA24310.1.
PIRiJV0051. DEECPP.
RefSeqiNP_416823.1. NC_000913.3.
WP_000699148.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75380; AAC75380; b2320.
BAA16177; BAA16177; BAA16177.
GeneIDi946785.
KEGGiecj:JW2317.
eco:b2320.
PATRICi32120013. VBIEscCol129921_2416.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M29962 Genomic DNA. Translation: AAA24308.1.
U76961 Genomic DNA. Translation: AAB36530.1.
U00096 Genomic DNA. Translation: AAC75380.1.
AP009048 Genomic DNA. Translation: BAA16177.1.
X02743 Genomic DNA. Translation: CAA26520.1.
M15541 Genomic DNA. Translation: AAA24310.1.
PIRiJV0051. DEECPP.
RefSeqiNP_416823.1. NC_000913.3.
WP_000699148.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP05459.
SMRiP05459.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259616. 19 interactors.
DIPiDIP-10449N.
IntActiP05459. 9 interactors.
STRINGi511145.b2320.

Proteomic databases

EPDiP05459.
PaxDbiP05459.
PRIDEiP05459.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75380; AAC75380; b2320.
BAA16177; BAA16177; BAA16177.
GeneIDi946785.
KEGGiecj:JW2317.
eco:b2320.
PATRICi32120013. VBIEscCol129921_2416.

Organism-specific databases

EchoBASEiEB0686.
EcoGeneiEG10692. pdxB.

Phylogenomic databases

eggNOGiENOG4105CJ0. Bacteria.
COG0111. LUCA.
HOGENOMiHOG000234432.
InParanoidiP05459.
KOiK03473.
OMAiSAPGCNA.
PhylomeDBiP05459.

Enzyme and pathway databases

UniPathwayiUPA00244; UER00310.
BioCyciEcoCyc:ERYTHRON4PDEHYDROG-MONOMER.
ECOL316407:JW2317-MONOMER.
MetaCyc:ERYTHRON4PDEHYDROG-MONOMER.
BRENDAi1.1.1.290. 2026.

Miscellaneous databases

PROiP05459.

Family and domain databases

CDDicd12158. ErythrP_dh. 1 hit.
Gene3Di3.40.50.720. 2 hits.
HAMAPiMF_01825. PdxB. 1 hit.
InterProiIPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR029753. D-isomer_DH_CS.
IPR029752. D-isomer_DH_CS1.
IPR006140. D-isomer_DH_NAD-bd.
IPR020921. Erythronate-4-P_DHase.
IPR024531. Erythronate-4-P_DHase_dimer.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERiPTHR10996:SF111. PTHR10996:SF111. 1 hit.
PfamiPF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
PF11890. DUF3410. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
PROSITEiPS00065. D_2_HYDROXYACID_DH_1. 1 hit.
PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPDXB_ECOLI
AccessioniPrimary (citable) accession number: P05459
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1988
Last sequence update: April 1, 1990
Last modified: November 2, 2016
This is version 148 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.