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P0A794 (PDXJ_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 88. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Pyridoxine 5'-phosphate synthase

Short name=PNP synthase
EC=2.6.99.2
Gene names
Name:pdxJ
Ordered Locus Names:b2564, JW2548
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length243 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate. Ref.7

Catalytic activity

1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O. HAMAP-Rule MF_00279

Pathway

Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 5/5. HAMAP-Rule MF_00279

Subunit structure

Homooctamer; tetramer of dimers. Ref.10 Ref.11

Subcellular location

Cytoplasm HAMAP-Rule MF_00279.

Sequence similarities

Belongs to the PNP synthase family.

Sequence caution

The sequence D64044 differs from that shown. Reason: Frameshift at several positions.

Ontologies

Keywords
   Biological processPyridoxine biosynthesis
   Cellular componentCytoplasm
   Molecular functionTransferase
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processpyridoxine biosynthetic process

Inferred from mutant phenotype Ref.1. Source: EcoliWiki

   Cellular_componentcytosol

Inferred from direct assay PubMed 16858726. Source: UniProtKB

   Molecular_functionpyridoxine 5'-phosphate synthase activity

Inferred from direct assay Ref.7. Source: EcoCyc

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed HAMAP-Rule MF_00279
Chain2 – 243242Pyridoxine 5'-phosphate synthase HAMAP-Rule MF_00279
PRO_0000190114

Regions

Region11 – 1221-deoxy-D-xylulose 5-phosphate binding HAMAP-Rule MF_00279
Region215 – 21623-amino-2-oxopropyl phosphate binding HAMAP-Rule MF_00279

Sites

Active site451Proton acceptor
Active site721Proton acceptor
Active site1931Proton donor
Binding site913-amino-2-oxopropyl phosphate
Binding site2013-amino-2-oxopropyl phosphate
Binding site4711-deoxy-D-xylulose 5-phosphate
Binding site5211-deoxy-D-xylulose 5-phosphate
Binding site10211-deoxy-D-xylulose 5-phosphate
Binding site19413-amino-2-oxopropyl phosphate; via amide nitrogen
Site1531Transition state stabilizer

Natural variations

Natural variant1941G → S in pdxH null mutation suppressor. Ref.6

Secondary structure

.................................................. 243
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0A794 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: BF513A5B844E8CB2

FASTA24326,384
        10         20         30         40         50         60 
MAELLLGVNI DHIATLRNAR GTAYPDPVQA AFIAEQAGAD GITVHLREDR RHITDRDVRI 

        70         80         90        100        110        120 
LRQTLDTRMN LEMAVTEEML AIAVETKPHF CCLVPEKRQE VTTEGGLDVA GQRDKMRDAC 

       130        140        150        160        170        180 
KRLADAGIQV SLFIDADEEQ IKAAAEVGAP FIEIHTGCYA DAKTDAEQAQ ELARIAKAAT 

       190        200        210        220        230        240 
FAASLGLKVN AGHGLTYHNV KAIAAIPEMH ELNIGHAIIG RAVMTGLKDA VAEMKRLMLE 


ARG 

« Hide

References

« Hide 'large scale' references
[1]"Locating essential Escherichia coli genes by using mini-Tn10 transposons: the pdxJ operon."
Takiff H.E., Baker T., Copeland T., Chen S.-M., Court D.L.
J. Bacteriol. 174:1544-1553(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
Strain: K12.
[2]"Suppression of insertions in the complex pdxJ operon of Escherichia coli K-12 by lon and other mutations."
Lam H.-M., Tancula E., Dempsey W.B., Winkler M.E.
J. Bacteriol. 174:1554-1567(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[3]Nashimoto H., Saito N.
Submitted (SEP-1995) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[4]"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 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[5]"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.
[6]"Isolation of a pdxJ point mutation that bypasses the requirement for the PdxH oxidase in pyridoxal 5'-phosphate coenzyme biosynthesis in Escherichia coli K-12."
Man T.K., Zhao G., Winkler M.E.
J. Bacteriol. 178:2445-2449(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT SER-194.
[7]"Vitamin B6 biosynthesis: formation of pyridoxine 5'-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein."
Laber B., Maurer W., Scharf S., Stepusin K., Schmidt F.S.
FEBS Lett. 449:45-48(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
Strain: K12 / ATCC 35607 / JM83.
[8]"Crystallization and preliminary X-ray crystallographic analysis of PdxJ, the pyridoxine 5'-phosphate synthesizing enzyme."
Garrido Franco M., Huber R., Schmidt F.S., Laber B., Clausen T.
Acta Crystallogr. D 56:1045-1048(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: CRYSTALLIZATION.
[9]"Pyridoxine 5'-phosphate synthase: de novo synthesis of vitamin B6 and beyond."
Garrido-Franco M.
Biochim. Biophys. Acta 1647:92-97(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
[10]"Structural basis for the function of pyridoxine 5'-phosphate synthase."
Garrido Franco M., Laber B., Huber R., Clausen T.
Structure 9:245-253(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH PRODUCT, SUBUNIT.
[11]"Multistate binding in pyridoxine 5'-phosphate synthase: 1.96 A crystal structure in complex with 1-deoxy-D-xylulose phosphate."
Yeh J.I., Du S., Pohl E., Cane D.E.
Biochemistry 41:11649-11657(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) OF APOENZYME AND COMPLEX WITH SUBSTRATE, SUBUNIT.
[12]"Enzyme-ligand complexes of pyridoxine 5'-phosphate synthase: implications for substrate binding and catalysis."
Garrido-Franco M., Laber B., Huber R., Clausen T.
J. Mol. Biol. 321:601-612(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE AND SUBSTRATE ANALOG, REACTION MECHANISM.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M76470 Genomic DNA. Translation: AAA21845.1.
M74526 Genomic DNA. Translation: AAA24315.1.
D64044 Genomic DNA. No translation available.
U36841 Genomic DNA. Translation: AAA79826.1.
U00096 Genomic DNA. Translation: AAC75617.1.
AP009048 Genomic DNA. Translation: BAE76740.1.
PIRA42293.
RefSeqNP_417059.1. NC_000913.3.
YP_490792.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1HO1X-ray2.00A/B/C/D2-243[»]
1HO4X-ray2.30A/B/C/D2-243[»]
1IXNX-ray2.30A/B/C/D2-243[»]
1IXOX-ray2.30A/B/C/D2-243[»]
1IXPX-ray2.30A/B/C/D2-243[»]
1IXQX-ray2.30A/B/C/D2-243[»]
1M5WX-ray1.96A/B/C/D/E/F/G/H1-243[»]
ProteinModelPortalP0A794.
SMRP0A794. Positions 2-243.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-36215N.
IntActP0A794. 5 interactions.
MINTMINT-1227457.
STRING511145.b2564.

Proteomic databases

PaxDbP0A794.
PRIDEP0A794.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75617; AAC75617; b2564.
BAE76740; BAE76740; BAE76740.
GeneID12931607.
947039.
KEGGecj:Y75_p2517.
eco:b2564.
PATRIC32120527. VBIEscCol129921_2666.

Organism-specific databases

EchoBASEEB0687.
EcoGeneEG10693. pdxJ.

Phylogenomic databases

eggNOGCOG0854.
HOGENOMHOG000258095.
KOK03474.
OMAVPETRQE.
OrthoDBEOG6M9F0H.
PhylomeDBP0A794.

Enzyme and pathway databases

BioCycEcoCyc:PDXJ-MONOMER.
ECOL316407:JW2548-MONOMER.
MetaCyc:PDXJ-MONOMER.
UniPathwayUPA00244; UER00313.

Gene expression databases

GenevestigatorP0A794.

Family and domain databases

Gene3D3.20.20.70. 1 hit.
HAMAPMF_00279. PdxJ.
InterProIPR013785. Aldolase_TIM.
IPR004569. PyrdxlP_synth_PdxJ.
[Graphical view]
PfamPF03740. PdxJ. 1 hit.
[Graphical view]
SUPFAMSSF63892. SSF63892. 1 hit.
TIGRFAMsTIGR00559. pdxJ. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP0A794.
PROP0A794.

Entry information

Entry namePDXJ_ECOLI
AccessionPrimary (citable) accession number: P0A794
Secondary accession number(s): P24223, Q2MAG6
Entry history
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: January 23, 2007
Last modified: May 14, 2014
This is version 88 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

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