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Protein

4-hydroxythreonine-4-phosphate dehydrogenase

Gene

pdxA

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

Functioni

Catalyzes the NAD(P)-dependent oxidation of 4-(phosphohydroxy)-L-threonine (HTP) into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which spontaneously decarboxylates to form 3-amino-2-oxopropyl phosphate (AHAP).2 Publications

Catalytic activityi

4-phosphonooxy-L-threonine + NAD+ = 3-amino-2-oxopropyl phosphate + CO2 + NADH.1 Publication

Cofactori

Zn2+2 Publications, Mg2+2 Publications, Co2+2 PublicationsNote: Binds 1 divalent metal cation per subunit. Can use ions such as Zn2+, Mg2+ or Co2+.2 Publications

Kineticsi

  1. KM=85 µM for 4-(phosphohydroxy)-L-threonine (at 0.1 M Tris-HCl and pH 7.5)1 Publication
  2. KM=113 µM for 4-(phosphohydroxy)-L-threonine (at 0.1 M phosphate buffer and pH 7.5)1 Publication
  1. Vmax=2.8 µmol/min/mg enzyme with 4-(phosphohydroxy)-L-threonine as substrate (at 0.1 M Tris-HCl and pH 7.5)1 Publication
  2. Vmax=0.66 µmol/min/mg enzyme with 4-(phosphohydroxy)-L-threonine as substrate (at 0.1 M phosphate buffer and pH 7.5)1 Publication

Pathwayi: pyridoxine 5'-phosphate biosynthesis

This protein is involved in step 4 of the subpathway that synthesizes pyridoxine 5'-phosphate from D-erythrose 4-phosphate.
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 sitei136Substrate1 Publication1
Binding sitei137Substrate1 Publication1
Metal bindingi166Divalent metal cation; shared with dimeric partner1
Metal bindingi211Divalent metal cation; shared with dimeric partner1
Metal bindingi266Divalent metal cation; shared with dimeric partner1
Binding sitei274Substrate1 Publication1
Binding sitei283Substrate1 Publication1
Binding sitei292Substrate1 Publication1

GO - Molecular functioni

  • 4-hydroxythreonine-4-phosphate dehydrogenase activity Source: EcoCyc
  • cobalt ion binding Source: UniProtKB-HAMAP
  • magnesium ion binding Source: EcoCyc
  • NAD binding Source: EcoCyc
  • zinc ion binding Source: EcoCyc

GO - Biological processi

  • pyridoxal phosphate biosynthetic process Source: EcoCyc
  • pyridoxine biosynthetic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Pyridoxine biosynthesis

Keywords - Ligandi

Cobalt, Magnesium, Metal-binding, NAD, NADP, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:PDXA-MONOMER.
ECOL316407:JW0051-MONOMER.
MetaCyc:PDXA-MONOMER.
BRENDAi1.1.1.262. 2026.
UniPathwayiUPA00244; UER00312.

Names & Taxonomyi

Protein namesi
Recommended name:
4-hydroxythreonine-4-phosphate dehydrogenase (EC:1.1.1.262)
Alternative name(s):
4-(phosphohydroxy)-L-threonine dehydrogenase
Gene namesi
Name:pdxA
Ordered Locus Names:b0052, JW0051
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10691. pdxA.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001888041 – 3294-hydroxythreonine-4-phosphate dehydrogenaseAdd BLAST329

Proteomic databases

EPDiP19624.
PaxDbiP19624.
PRIDEiP19624.

Interactioni

Subunit structurei

Homodimer.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
itself3EBI-1112869,EBI-1112869

Protein-protein interaction databases

BioGridi4261013. 5 interactors.
DIPiDIP-10448N.
IntActiP19624. 5 interactors.
STRINGi511145.b0052.

Structurei

Secondary structure

1329
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 10Combined sources5
Helixi18 – 25Combined sources8
Beta strandi31 – 38Combined sources8
Helixi40 – 49Combined sources10
Beta strandi55 – 58Combined sources4
Beta strandi72 – 77Combined sources6
Helixi93 – 109Combined sources17
Beta strandi114 – 118Combined sources5
Helixi123 – 128Combined sources6
Helixi136 – 143Combined sources8
Beta strandi150 – 157Combined sources8
Beta strandi159 – 164Combined sources6
Helixi169 – 171Combined sources3
Helixi172 – 175Combined sources4
Helixi178 – 194Combined sources17
Beta strandi202 – 206Combined sources5
Helixi210 – 216Combined sources7
Helixi221 – 224Combined sources4
Helixi226 – 235Combined sources10
Beta strandi239 – 244Combined sources6
Helixi246 – 249Combined sources4
Helixi252 – 255Combined sources4
Beta strandi259 – 265Combined sources7
Helixi266 – 274Combined sources9
Beta strandi278 – 280Combined sources3
Beta strandi282 – 294Combined sources13
Helixi301 – 303Combined sources3
Turni304 – 306Combined sources3
Helixi312 – 328Combined sources17

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1PS6X-ray2.25A/B2-329[»]
1PS7X-ray2.47A/B/C/D1-329[»]
1PTMX-ray1.96A/B1-329[»]
ProteinModelPortaliP19624.
SMRiP19624.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP19624.

Family & Domainsi

Sequence similaritiesi

Belongs to the PdxA family.Curated

Phylogenomic databases

eggNOGiENOG4105CEZ. Bacteria.
COG1995. LUCA.
HOGENOMiHOG000221592.
InParanoidiP19624.
KOiK00097.
OMAiYVWDTPL.
PhylomeDBiP19624.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
HAMAPiMF_00536. PdxA. 1 hit.
InterProiIPR024084. IsoPropMal-DH-like_dom.
IPR005255. PdxA.
[Graphical view]
PfamiPF04166. PdxA. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00557. pdxA. 1 hit.

Sequencei

Sequence statusi: Complete.

P19624-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVKTQRVVIT PGEPAGIGPD LVVQLAQREW PVELVVCADA TLLTNRAAML
60 70 80 90 100
GLPLTLRPYS PNSPAQPQTA GTLTLLPVAL RAPVTAGQLA VENGHYVVET
110 120 130 140 150
LARACDGCLN GEFAALITGP VHKGVINDAG IPFTGHTEFF EERSQAKKVV
160 170 180 190 200
MMLATEELRV ALATTHLPLR DIADAITPAL LHEVIAILHH DLRTKFGIAE
210 220 230 240 250
PRILVCGLNP HAGEGGHMGT EEIDTIIPVL NELRAQGMKL NGPLPADTLF
260 270 280 290 300
QPKYLDNADA VLAMYHDQGL PVLKYQGFGR GVNITLGLPF IRTSVDHGTA
310 320
LELAGRGKAD VGSFITALNL AIKMIVNTQ
Length:329
Mass (Da):35,114
Last modified:February 1, 1991 - v1
Checksum:i44E1FEE233C86233
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M68521 Genomic DNA. Translation: AAA24305.1.
U00096 Genomic DNA. Translation: AAC73163.1.
AP009048 Genomic DNA. Translation: BAB96619.1.
PIRiJV0026. BVECXA.
RefSeqiNP_414594.1. NC_000913.3.
WP_000241277.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73163; AAC73163; b0052.
BAB96619; BAB96619; BAB96619.
GeneIDi944919.
KEGGiecj:JW0051.
eco:b0052.
PATRICi32115203. VBIEscCol129921_0053.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M68521 Genomic DNA. Translation: AAA24305.1.
U00096 Genomic DNA. Translation: AAC73163.1.
AP009048 Genomic DNA. Translation: BAB96619.1.
PIRiJV0026. BVECXA.
RefSeqiNP_414594.1. NC_000913.3.
WP_000241277.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1PS6X-ray2.25A/B2-329[»]
1PS7X-ray2.47A/B/C/D1-329[»]
1PTMX-ray1.96A/B1-329[»]
ProteinModelPortaliP19624.
SMRiP19624.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261013. 5 interactors.
DIPiDIP-10448N.
IntActiP19624. 5 interactors.
STRINGi511145.b0052.

Proteomic databases

EPDiP19624.
PaxDbiP19624.
PRIDEiP19624.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73163; AAC73163; b0052.
BAB96619; BAB96619; BAB96619.
GeneIDi944919.
KEGGiecj:JW0051.
eco:b0052.
PATRICi32115203. VBIEscCol129921_0053.

Organism-specific databases

EchoBASEiEB0685.
EcoGeneiEG10691. pdxA.

Phylogenomic databases

eggNOGiENOG4105CEZ. Bacteria.
COG1995. LUCA.
HOGENOMiHOG000221592.
InParanoidiP19624.
KOiK00097.
OMAiYVWDTPL.
PhylomeDBiP19624.

Enzyme and pathway databases

UniPathwayiUPA00244; UER00312.
BioCyciEcoCyc:PDXA-MONOMER.
ECOL316407:JW0051-MONOMER.
MetaCyc:PDXA-MONOMER.
BRENDAi1.1.1.262. 2026.

Miscellaneous databases

EvolutionaryTraceiP19624.
PROiP19624.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
HAMAPiMF_00536. PdxA. 1 hit.
InterProiIPR024084. IsoPropMal-DH-like_dom.
IPR005255. PdxA.
[Graphical view]
PfamiPF04166. PdxA. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00557. pdxA. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiPDXA_ECOLI
AccessioniPrimary (citable) accession number: P19624
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: February 1, 1991
Last modified: November 2, 2016
This is version 148 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The active site is located at the dimer interface.
According to PubMed:15026039, PdxA may catalyze both oxidation and decarboxylation reactions that directly lead to AHAP.

Keywords - Technical termi

3D-structure, 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.