4-hydroxythreonine-4-phosphate dehydrogenase - Escherichia coli (strain K12)

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P19624 (PDXA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 122. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
4-hydroxythreonine-4-phosphate dehydrogenase
EC=1.1.1.262

Alternative name(s):
4-(phosphohydroxy)-L-threonine dehydrogenase

Gene names

Name:	pdxA
Ordered Locus Names:	b0052, JW0051

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	329 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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). Ref.5 Ref.6
Catalytic activity	4-phosphonooxy-L-threonine + NAD⁺ = 3-amino-2-oxopropyl phosphate + CO₂ + NADH. Ref.6
Cofactor	Binds 1 divalent metal cation per subunit. Can use ions such as zinc, magnesium or cobalt. Ref.5 Ref.7
Pathway	Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 4/5. HAMAP-Rule MF_00536
Subunit structure	Homodimer. Ref.7
Subcellular location	Cytoplasm By similarity.
Miscellaneous	The active site is located at the dimer interface. HAMAP-Rule MF_00536 According to Ref.6, PdxA may catalyze both oxidation and decarboxylation reactions that directly lead to AHAP. HAMAP-Rule MF_00536
Sequence similarities	Belongs to the PdxA family.
Biophysicochemical properties	Kinetic parameters: K_M=85 µM for 4-(phosphohydroxy)-L-threonine (at 0.1 M Tris-HCl and pH 7.5) Ref.5 K_M=113 µM for 4-(phosphohydroxy)-L-threonine (at 0.1 M phosphate buffer and pH 7.5) V_max=2.8 µmol/min/mg enzyme with 4-(phosphohydroxy)-L-threonine as substrate (at 0.1 M Tris-HCl and pH 7.5) V_max=0.66 µmol/min/mg enzyme with 4-(phosphohydroxy)-L-threonine as substrate (at 0.1 M phosphate buffer and pH 7.5)

Ontologies

Keywords
Biological process	Pyridoxine biosynthesis
Cellular component	Cytoplasm
Ligand	Cobalt Magnesium Metal-binding NAD NADP Zinc
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	pyridoxal phosphate biosynthetic process Inferred from mutant phenotype PubMed 1537800. Source: EcoCyc pyridoxine biosynthetic process Inferred from mutant phenotype PubMed 1537800. Source: EcoCyc
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	4-hydroxythreonine-4-phosphate dehydrogenase activity Inferred from direct assay Ref.6. Source: EcoCyc NAD binding Inferred from direct assay Ref.7. Source: EcoCyc cobalt ion binding Inferred from electronic annotation. Source: HAMAP magnesium ion binding Inferred from direct assay Ref.6. Source: EcoCyc zinc ion binding Inferred from direct assay Ref.7 Ref.6. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 329

329

4-hydroxythreonine-4-phosphate dehydrogenase HAMAP-Rule MF_00536

PRO_0000188804

Sites

Metal binding

166

Divalent metal cation; shared with dimeric partner

Metal binding

211

Divalent metal cation; shared with dimeric partner

Metal binding

266

Divalent metal cation; shared with dimeric partner

Binding site

136

Substrate

Binding site

137

Substrate

Binding site

274

Substrate

Binding site

283

Substrate

Binding site

292

Substrate

Secondary structure

329

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P19624 [UniParc].

Last modified February 1, 1991. Version 1.
Checksum: 44E1FEE233C86233
Show »

FASTA

329

35,114

        10         20         30         40         50         60 
MVKTQRVVIT PGEPAGIGPD LVVQLAQREW PVELVVCADA TLLTNRAAML GLPLTLRPYS 

        70         80         90        100        110        120 
PNSPAQPQTA GTLTLLPVAL RAPVTAGQLA VENGHYVVET LARACDGCLN GEFAALITGP 

       130        140        150        160        170        180 
VHKGVINDAG IPFTGHTEFF EERSQAKKVV MMLATEELRV ALATTHLPLR DIADAITPAL 

       190        200        210        220        230        240 
LHEVIAILHH DLRTKFGIAE PRILVCGLNP HAGEGGHMGT EEIDTIIPVL NELRAQGMKL 

       250        260        270        280        290        300 
NGPLPADTLF QPKYLDNADA VLAMYHDQGL PVLKYQGFGR GVNITLGLPF IRTSVDHGTA 

       310        320 
LELAGRGKAD VGSFITALNL AIKMIVNTQ

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract] 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M68521 Genomic DNA. Translation: AAA24305.1.
U00096 Genomic DNA. Translation: AAC73163.1.
AP009048 Genomic DNA. Translation: BAB96619.1.

PIR

BVECXA. JV0026.

RefSeq

NP_414594.1. NC_000913.2.
YP_488358.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P19624.

SMR

P19624. Positions 1-329.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10448N.

IntAct

P19624. 2 interactions.

STRING

511145.b0052.

Proteomic databases

PaxDb

P19624.

PRIDE

P19624.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC73163; AAC73163; b0052.
BAB96619; BAB96619; BAB96619.

GeneID

12932019.
944919.

KEGG

ecj:Y75_p0052.
eco:b0052.

PATRIC

32115203. VBIEscCol129921_0053.

Organism-specific databases

EchoBASE

EB0685.

EcoGene

EG10691. pdxA.

Phylogenomic databases

eggNOG

COG1995.

HOGENOM

HOG000221592.

K00097.

OMA

RITHAAM.

ProtClustDB

PRK00232.

Enzyme and pathway databases

BioCyc

EcoCyc:PDXA-MONOMER.
ECOL316407:JW0051-MONOMER.
MetaCyc:PDXA-MONOMER.

UniPathway

UPA00244; UER00312.

Gene expression databases

Genevestigator

P19624.

Family and domain databases

Gene3D

3.40.718.10. 1 hit.

HAMAP

MF_00536. PdxA.

InterPro

IPR024084. IsoPropMal-DH-like_dom.
IPR005255. PyrdxlP_synth_PdxA.
[Graphical view]

Pfam

PF04166. PdxA. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00557. pdxA. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

P19624.

Entry information

Entry name

PDXA_ECOLI

Accession

Primary (citable) accession number: P19624

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1991
Last sequence update:	February 1, 1991
Last modified:	May 1, 2013
This is version 122 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents