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P19624

- PDXA_ECOLI

UniProt

P19624 - PDXA_ECOLI

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Protein
4-hydroxythreonine-4-phosphate dehydrogenase
Gene
pdxA, b0052, JW0051
Organism
Escherichia coli (strain K12)
Status
Reviewed - 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

Binds 1 divalent metal cation per subunit. Can use ions such as zinc, magnesium or cobalt.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)

Vmax=2.8 µmol/min/mg enzyme with 4-(phosphohydroxy)-L-threonine as substrate (at 0.1 M Tris-HCl and pH 7.5)

Vmax=0.66 µmol/min/mg enzyme with 4-(phosphohydroxy)-L-threonine as substrate (at 0.1 M phosphate buffer and pH 7.5)

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei136 – 1361Substrate
Binding sitei137 – 1371Substrate
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 – 2741Substrate
Binding sitei283 – 2831Substrate
Binding sitei292 – 2921Substrate

GO - Molecular functioni

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

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 UniRule annotation

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 dehydrogenaseUniRule annotation
PRO_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

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 105
Helixi18 – 258
Beta strandi31 – 388
Helixi40 – 4910
Beta strandi55 – 584
Beta strandi72 – 776
Helixi93 – 10917
Beta strandi114 – 1185
Helixi123 – 1286
Helixi136 – 1438
Beta strandi150 – 1578
Beta strandi159 – 1646
Helixi169 – 1713
Helixi172 – 1754
Helixi178 – 19417
Beta strandi202 – 2065
Helixi210 – 2167
Helixi221 – 2244
Helixi226 – 23510
Beta strandi239 – 2446
Helixi246 – 2494
Helixi252 – 2554
Beta strandi259 – 2657
Helixi266 – 2749
Beta strandi278 – 2803
Beta strandi282 – 29413
Helixi301 – 3033
Turni304 – 3063
Helixi312 – 32817

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.

Miscellaneous databases

EvolutionaryTraceiP19624.

Family & Domainsi

Sequence similaritiesi

Belongs to the PdxA family.

Phylogenomic databases

eggNOGiCOG1995.
HOGENOMiHOG000221592.
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

MVKTQRVVIT PGEPAGIGPD LVVQLAQREW PVELVVCADA TLLTNRAAML    50
GLPLTLRPYS PNSPAQPQTA GTLTLLPVAL RAPVTAGQLA VENGHYVVET 100
LARACDGCLN GEFAALITGP VHKGVINDAG IPFTGHTEFF EERSQAKKVV 150
MMLATEELRV ALATTHLPLR DIADAITPAL LHEVIAILHH DLRTKFGIAE 200
PRILVCGLNP HAGEGGHMGT EEIDTIIPVL NELRAQGMKL NGPLPADTLF 250
QPKYLDNADA VLAMYHDQGL PVLKYQGFGR GVNITLGLPF IRTSVDHGTA 300
LELAGRGKAD VGSFITALNL AIKMIVNTQ 329
Length:329
Mass (Da):35,114
Last modified:February 1, 1991 - v1
Checksum:i44E1FEE233C86233
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
M68521 Genomic DNA. Translation: AAA24305.1 .
U00096 Genomic DNA. Translation: AAC73163.1 .
AP009048 Genomic DNA. Translation: BAB96619.1 .
PIRi JV0026. BVECXA.
RefSeqi NP_414594.1. NC_000913.3.
YP_488358.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1PS6 X-ray 2.25 A/B 2-329 [» ]
1PS7 X-ray 2.47 A/B/C/D 1-329 [» ]
1PTM X-ray 1.96 A/B 1-329 [» ]
ProteinModelPortali P19624.
SMRi P19624. Positions 1-329.
ModBasei Search...

Protein-protein interaction databases

DIPi DIP-10448N.
IntActi P19624. 5 interactions.
STRINGi 511145.b0052.

Proteomic databases

PaxDbi P19624.
PRIDEi P19624.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC73163 ; AAC73163 ; b0052 .
BAB96619 ; BAB96619 ; BAB96619 .
GeneIDi 12932019.
944919.
KEGGi ecj:Y75_p0052.
eco:b0052.
PATRICi 32115203. VBIEscCol129921_0053.

Organism-specific databases

EchoBASEi EB0685.
EcoGenei EG10691. pdxA.

Phylogenomic databases

eggNOGi COG1995.
HOGENOMi HOG000221592.
KOi K00097.
OMAi DTLFQDK.
OrthoDBi EOG6GN6ZC.
PhylomeDBi P19624.

Enzyme and pathway databases

UniPathwayi UPA00244 ; UER00312 .
BioCyci EcoCyc:PDXA-MONOMER.
ECOL316407:JW0051-MONOMER.
MetaCyc:PDXA-MONOMER.

Miscellaneous databases

EvolutionaryTracei P19624.
PROi P19624.

Gene expression databases

Genevestigatori P19624.

Family and domain databases

Gene3Di 3.40.718.10. 1 hit.
HAMAPi MF_00536. PdxA.
InterProi IPR024084. IsoPropMal-DH-like_dom.
IPR005255. PdxA.
[Graphical view ]
Pfami PF04166. PdxA. 1 hit.
[Graphical view ]
TIGRFAMsi TIGR00557. pdxA. 1 hit.
ProtoNeti Search...

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: July 9, 2014
This is version 132 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 1 Publication, 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

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