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P0A794

- PDXJ_ECOLI

UniProt

P0A794 - PDXJ_ECOLI

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Protein

Pyridoxine 5'-phosphate synthase

Gene

pdxJ

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

Functioni

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.1 Publication

Catalytic activityi

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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei9 – 913-amino-2-oxopropyl phosphate
Binding sitei20 – 2013-amino-2-oxopropyl phosphate
Active sitei45 – 451Proton acceptor
Binding sitei47 – 4711-deoxy-D-xylulose 5-phosphate
Binding sitei52 – 5211-deoxy-D-xylulose 5-phosphate
Active sitei72 – 721Proton acceptor
Binding sitei102 – 10211-deoxy-D-xylulose 5-phosphate
Sitei153 – 1531Transition state stabilizer
Active sitei193 – 1931Proton donor
Binding sitei194 – 19413-amino-2-oxopropyl phosphate; via amide nitrogen

GO - Molecular functioni

  1. pyridoxine 5'-phosphate synthase activity Source: EcoCyc

GO - Biological processi

  1. pyridoxine biosynthetic process Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Pyridoxine biosynthesis

Enzyme and pathway databases

BioCyciEcoCyc:PDXJ-MONOMER.
ECOL316407:JW2548-MONOMER.
MetaCyc:PDXJ-MONOMER.
UniPathwayiUPA00244; UER00313.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxine 5'-phosphate synthase (EC:2.6.99.2)
Short name:
PNP synthase
Gene namesi
Name:pdxJ
Ordered Locus Names:b2564, JW2548
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10693. pdxJ.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed
Chaini2 – 243242Pyridoxine 5'-phosphate synthasePRO_0000190114Add
BLAST

Proteomic databases

PaxDbiP0A794.
PRIDEiP0A794.

Expressioni

Gene expression databases

GenevestigatoriP0A794.

Interactioni

Subunit structurei

Homooctamer; tetramer of dimers.2 Publications

Protein-protein interaction databases

DIPiDIP-36215N.
IntActiP0A794. 5 interactions.
MINTiMINT-1227457.
STRINGi511145.b2564.

Structurei

Secondary structure

1
243
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 95Combined sources
Helixi11 – 188Combined sources
Beta strandi20 – 223Combined sources
Helixi27 – 359Combined sources
Turni36 – 383Combined sources
Beta strandi40 – 456Combined sources
Beta strandi51 – 533Combined sources
Helixi55 – 6410Combined sources
Beta strandi66 – 738Combined sources
Helixi77 – 8610Combined sources
Beta strandi89 – 935Combined sources
Turni98 – 1003Combined sources
Beta strandi103 – 1053Combined sources
Helixi110 – 1123Combined sources
Helixi113 – 12513Combined sources
Beta strandi129 – 1346Combined sources
Helixi138 – 1469Combined sources
Beta strandi150 – 1556Combined sources
Helixi157 – 1615Combined sources
Helixi165 – 18420Combined sources
Beta strandi188 – 1947Combined sources
Turni197 – 1993Combined sources
Helixi200 – 2045Combined sources
Beta strandi209 – 2146Combined sources
Helixi216 – 22510Combined sources
Helixi227 – 24216Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliP0A794.
SMRiP0A794. Positions 2-243.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A794.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni11 – 1221-deoxy-D-xylulose 5-phosphate binding
Regioni215 – 21623-amino-2-oxopropyl phosphate binding

Sequence similaritiesi

Belongs to the PNP synthase family.Curated

Phylogenomic databases

eggNOGiCOG0854.
HOGENOMiHOG000258095.
InParanoidiP0A794.
KOiK03474.
OMAiVPETRQE.
OrthoDBiEOG6M9F0H.
PhylomeDBiP0A794.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00279. PdxJ.
InterProiIPR013785. Aldolase_TIM.
IPR004569. PyrdxlP_synth_PdxJ.
[Graphical view]
PfamiPF03740. PdxJ. 1 hit.
[Graphical view]
SUPFAMiSSF63892. SSF63892. 1 hit.
TIGRFAMsiTIGR00559. pdxJ. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A794-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MAELLLGVNI DHIATLRNAR GTAYPDPVQA AFIAEQAGAD GITVHLREDR
60 70 80 90 100
RHITDRDVRI LRQTLDTRMN LEMAVTEEML AIAVETKPHF CCLVPEKRQE
110 120 130 140 150
VTTEGGLDVA GQRDKMRDAC KRLADAGIQV SLFIDADEEQ IKAAAEVGAP
160 170 180 190 200
FIEIHTGCYA DAKTDAEQAQ ELARIAKAAT FAASLGLKVN AGHGLTYHNV
210 220 230 240
KAIAAIPEMH ELNIGHAIIG RAVMTGLKDA VAEMKRLMLE ARG
Length:243
Mass (Da):26,384
Last modified:January 23, 2007 - v2
Checksum:iBF513A5B844E8CB2
GO

Sequence cautioni

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

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti194 – 1941G → S in pdxH null mutation suppressor. 1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
PIRiA42293.
RefSeqiNP_417059.1. NC_000913.3.
YP_490792.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC75617; AAC75617; b2564.
BAE76740; BAE76740; BAE76740.
GeneIDi12931607.
947039.
KEGGiecj:Y75_p2517.
eco:b2564.
PATRICi32120527. VBIEscCol129921_2666.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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 .
PIRi A42293.
RefSeqi NP_417059.1. NC_000913.3.
YP_490792.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1HO1 X-ray 2.00 A/B/C/D 2-243 [» ]
1HO4 X-ray 2.30 A/B/C/D 2-243 [» ]
1IXN X-ray 2.30 A/B/C/D 2-243 [» ]
1IXO X-ray 2.30 A/B/C/D 2-243 [» ]
1IXP X-ray 2.30 A/B/C/D 2-243 [» ]
1IXQ X-ray 2.30 A/B/C/D 2-243 [» ]
1M5W X-ray 1.96 A/B/C/D/E/F/G/H 1-243 [» ]
ProteinModelPortali P0A794.
SMRi P0A794. Positions 2-243.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-36215N.
IntActi P0A794. 5 interactions.
MINTi MINT-1227457.
STRINGi 511145.b2564.

Proteomic databases

PaxDbi P0A794.
PRIDEi P0A794.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC75617 ; AAC75617 ; b2564 .
BAE76740 ; BAE76740 ; BAE76740 .
GeneIDi 12931607.
947039.
KEGGi ecj:Y75_p2517.
eco:b2564.
PATRICi 32120527. VBIEscCol129921_2666.

Organism-specific databases

EchoBASEi EB0687.
EcoGenei EG10693. pdxJ.

Phylogenomic databases

eggNOGi COG0854.
HOGENOMi HOG000258095.
InParanoidi P0A794.
KOi K03474.
OMAi VPETRQE.
OrthoDBi EOG6M9F0H.
PhylomeDBi P0A794.

Enzyme and pathway databases

UniPathwayi UPA00244 ; UER00313 .
BioCyci EcoCyc:PDXJ-MONOMER.
ECOL316407:JW2548-MONOMER.
MetaCyc:PDXJ-MONOMER.

Miscellaneous databases

EvolutionaryTracei P0A794.
PROi P0A794.

Gene expression databases

Genevestigatori P0A794.

Family and domain databases

Gene3Di 3.20.20.70. 1 hit.
HAMAPi MF_00279. PdxJ.
InterProi IPR013785. Aldolase_TIM.
IPR004569. PyrdxlP_synth_PdxJ.
[Graphical view ]
Pfami PF03740. PdxJ. 1 hit.
[Graphical view ]
SUPFAMi SSF63892. SSF63892. 1 hit.
TIGRFAMsi TIGR00559. pdxJ. 1 hit.
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. 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.

Entry informationi

Entry nameiPDXJ_ECOLI
AccessioniPrimary (citable) accession number: P0A794
Secondary accession number(s): P24223, Q2MAG6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 7, 2005
Last sequence update: January 23, 2007
Last modified: November 26, 2014
This is version 91 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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