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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 Zn(2+), Mg(2+) 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

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

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei136 – 1361Substrate1 Publication
Binding sitei137 – 1371Substrate1 Publication
Metal bindingi166 – 1661Divalent metal cation; shared with dimeric partner
Metal bindingi211 – 2111Divalent metal cation; shared with dimeric partner
Metal bindingi266 – 2661Divalent metal cation; shared with dimeric partner
Binding sitei274 – 2741Substrate1 Publication
Binding sitei283 – 2831Substrate1 Publication
Binding sitei292 – 2921Substrate1 Publication

GO - Molecular functioni

  1. 4-hydroxythreonine-4-phosphate dehydrogenase activity Source: EcoCyc
  2. cobalt ion binding Source: UniProtKB-HAMAP
  3. identical protein binding Source: IntAct
  4. magnesium ion binding Source: EcoCyc
  5. NAD binding Source: EcoCyc
  6. zinc ion binding Source: EcoCyc

GO - Biological processi

  1. pyridoxal phosphate biosynthetic process Source: EcoCyc
  2. 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.
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10691. pdxA.

Subcellular locationi

Cytoplasm By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 3293294-hydroxythreonine-4-phosphate dehydrogenasePRO_0000188804Add
BLAST

Proteomic databases

PaxDbiP19624.
PRIDEiP19624.

Expressioni

Gene expression databases

GenevestigatoriP19624.

Interactioni

Subunit structurei

Homodimer.1 Publication

Binary interactionsi

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

Protein-protein interaction databases

DIPiDIP-10448N.
IntActiP19624. 5 interactions.
STRINGi511145.b0052.

Structurei

Secondary structure

1
329
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 105Combined sources
Helixi18 – 258Combined sources
Beta strandi31 – 388Combined sources
Helixi40 – 4910Combined sources
Beta strandi55 – 584Combined sources
Beta strandi72 – 776Combined sources
Helixi93 – 10917Combined sources
Beta strandi114 – 1185Combined sources
Helixi123 – 1286Combined sources
Helixi136 – 1438Combined sources
Beta strandi150 – 1578Combined sources
Beta strandi159 – 1646Combined sources
Helixi169 – 1713Combined sources
Helixi172 – 1754Combined sources
Helixi178 – 19417Combined sources
Beta strandi202 – 2065Combined sources
Helixi210 – 2167Combined sources
Helixi221 – 2244Combined sources
Helixi226 – 23510Combined sources
Beta strandi239 – 2446Combined sources
Helixi246 – 2494Combined sources
Helixi252 – 2554Combined sources
Beta strandi259 – 2657Combined sources
Helixi266 – 2749Combined sources
Beta strandi278 – 2803Combined sources
Beta strandi282 – 29413Combined sources
Helixi301 – 3033Combined sources
Helixi312 – 32817Combined sources

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP19624.

Family & Domainsi

Sequence similaritiesi

Belongs to the PdxA family.Curated

Phylogenomic databases

eggNOGiCOG1995.
HOGENOMiHOG000221592.
InParanoidiP19624.
KOiK00097.
OMAiDTLFQDK.
OrthoDBiEOG6GN6ZC.
PhylomeDBiP19624.

Family and domain databases

Gene3Di3.40.718.10. 1 hit.
HAMAPiMF_00536. PdxA.
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.
YP_488358.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC73163; AAC73163; b0052.
BAB96619; BAB96619; BAB96619.
GeneIDi12932019.
944919.
KEGGiecj:Y75_p0052.
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.
YP_488358.1. NC_007779.1.

3D structure databases

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

Protein-protein interaction databases

DIPiDIP-10448N.
IntActiP19624. 5 interactions.
STRINGi511145.b0052.

Proteomic databases

PaxDbiP19624.
PRIDEiP19624.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73163; AAC73163; b0052.
BAB96619; BAB96619; BAB96619.
GeneIDi12932019.
944919.
KEGGiecj:Y75_p0052.
eco:b0052.
PATRICi32115203. VBIEscCol129921_0053.

Organism-specific databases

EchoBASEiEB0685.
EcoGeneiEG10691. pdxA.

Phylogenomic databases

eggNOGiCOG1995.
HOGENOMiHOG000221592.
InParanoidiP19624.
KOiK00097.
OMAiDTLFQDK.
OrthoDBiEOG6GN6ZC.
PhylomeDBiP19624.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP19624.
PROiP19624.

Gene expression databases

GenevestigatoriP19624.

Family and domain databases

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

Publicationsi

« Hide 'large scale' publications
  1. "Overlap between pdxA and ksgA in the complex pdxA-ksgA-apaG-apaH operon of Escherichia coli K-12."
    Roa B.B., Connolly D.M., Winkler M.E.
    J. Bacteriol. 171:4767-4777(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. "Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region."
    Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A.
    Nucleic Acids Res. 20:3305-3308(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Biosynthesis of vitamin B6: the oxidation of 4-hydroxy-L-threonine 4-phosphate by pdxA."
    Cane D.E., Hsiung Y., Cornish J.A., Robinson J.K., Spenser I.D.
    J. Am. Chem. Soc. 120:1936-1937(1998)
    Cited for: FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR.
  6. "Biosynthesis of vitamin B6: direct identification of the product of the PdxA-catalyzed oxidation of 4-hydroxy-L-threonine-4-phosphate using electrospray ionization mass spectrometry."
    Banks J., Cane D.E.
    Bioorg. Med. Chem. Lett. 14:1633-1636(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.
  7. "Crystal structure of Escherichia coli PdxA, an enzyme involved in the pyridoxal phosphate biosynthesis pathway."
    Sivaraman J., Li Y., Banks J., Cane D.E., Matte A., Cygler M.
    J. Biol. Chem. 278:43682-43690(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND ZINC IONS, COFACTOR, SUBUNIT.

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: February 4, 2015
This is version 137 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

External Data

Dasty 3

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 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.