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Protein

Pyridoxine 5'-phosphate synthase

Gene

pdxJ

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: 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: pyridoxine 5'-phosphate biosynthesis

This protein is involved in step 5 of the subpathway that synthesizes pyridoxine 5'-phosphate from D-erythrose 4-phosphate.
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. D-erythrose-4-phosphate dehydrogenase (epd)
  2. Erythronate-4-phosphate dehydrogenase (pdxB)
  3. Phosphoserine aminotransferase (serC)
  4. 4-hydroxythreonine-4-phosphate dehydrogenase (pdxA)
  5. Pyridoxine 5'-phosphate synthase (pdxJ)
This subpathway is part of the pathway pyridoxine 5'-phosphate biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxine 5'-phosphate from D-erythrose 4-phosphate, the pathway pyridoxine 5'-phosphate biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei93-amino-2-oxopropyl phosphate1
Binding sitei203-amino-2-oxopropyl phosphate1
Active sitei45Proton acceptor1
Binding sitei471-deoxy-D-xylulose 5-phosphate1
Binding sitei521-deoxy-D-xylulose 5-phosphate1
Active sitei72Proton acceptor1
Binding sitei1021-deoxy-D-xylulose 5-phosphate1
Sitei153Transition state stabilizer1
Active sitei193Proton donor1
Binding sitei1943-amino-2-oxopropyl phosphate; via amide nitrogen1

GO - Molecular functioni

  • pyridoxine 5'-phosphate synthase activity Source: EcoCyc

GO - Biological processi

  • 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.
BRENDAi2.6.99.2. 2026.
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10693. pdxJ.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved
ChainiPRO_00001901142 – 243Pyridoxine 5'-phosphate synthaseAdd BLAST242

Proteomic databases

EPDiP0A794.
PaxDbiP0A794.
PRIDEiP0A794.

Interactioni

Subunit structurei

Homooctamer; tetramer of dimers.2 Publications

Protein-protein interaction databases

BioGridi4260601. 8 interactors.
DIPiDIP-36215N.
IntActiP0A794. 5 interactors.
MINTiMINT-1227457.
STRINGi511145.b2564.

Structurei

Secondary structure

1243
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 9Combined sources5
Helixi11 – 18Combined sources8
Beta strandi20 – 22Combined sources3
Helixi27 – 35Combined sources9
Turni36 – 38Combined sources3
Beta strandi40 – 45Combined sources6
Beta strandi51 – 53Combined sources3
Helixi55 – 64Combined sources10
Beta strandi66 – 73Combined sources8
Helixi77 – 86Combined sources10
Beta strandi89 – 93Combined sources5
Turni98 – 100Combined sources3
Beta strandi103 – 105Combined sources3
Helixi110 – 112Combined sources3
Helixi113 – 125Combined sources13
Beta strandi129 – 134Combined sources6
Helixi138 – 146Combined sources9
Beta strandi150 – 155Combined sources6
Helixi157 – 161Combined sources5
Helixi165 – 184Combined sources20
Beta strandi188 – 194Combined sources7
Turni197 – 199Combined sources3
Helixi200 – 204Combined sources5
Beta strandi209 – 214Combined sources6
Helixi216 – 225Combined sources10
Helixi227 – 242Combined sources16

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A794.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni11 – 121-deoxy-D-xylulose 5-phosphate binding2
Regioni215 – 2163-amino-2-oxopropyl phosphate binding2

Sequence similaritiesi

Belongs to the PNP synthase family.Curated

Phylogenomic databases

eggNOGiENOG4105CSZ. Bacteria.
COG0854. LUCA.
HOGENOMiHOG000258095.
InParanoidiP0A794.
KOiK03474.
OMAiERHIRYQ.
PhylomeDBiP0A794.

Family and domain databases

CDDicd00003. PNPsynthase. 1 hit.
Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00279. PdxJ. 1 hit.
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)DescriptionActionsGraphical viewLength
Natural varianti194G → S in pdxH null mutation suppressor. 1 Publication1

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.
WP_001297412.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75617; AAC75617; b2564.
BAE76740; BAE76740; BAE76740.
GeneIDi947039.
KEGGiecj:JW2548.
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.
PIRiA42293.
RefSeqiNP_417059.1. NC_000913.3.
WP_001297412.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260601. 8 interactors.
DIPiDIP-36215N.
IntActiP0A794. 5 interactors.
MINTiMINT-1227457.
STRINGi511145.b2564.

Proteomic databases

EPDiP0A794.
PaxDbiP0A794.
PRIDEiP0A794.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75617; AAC75617; b2564.
BAE76740; BAE76740; BAE76740.
GeneIDi947039.
KEGGiecj:JW2548.
eco:b2564.
PATRICi32120527. VBIEscCol129921_2666.

Organism-specific databases

EchoBASEiEB0687.
EcoGeneiEG10693. pdxJ.

Phylogenomic databases

eggNOGiENOG4105CSZ. Bacteria.
COG0854. LUCA.
HOGENOMiHOG000258095.
InParanoidiP0A794.
KOiK03474.
OMAiERHIRYQ.
PhylomeDBiP0A794.

Enzyme and pathway databases

UniPathwayiUPA00244; UER00313.
BioCyciEcoCyc:PDXJ-MONOMER.
ECOL316407:JW2548-MONOMER.
MetaCyc:PDXJ-MONOMER.
BRENDAi2.6.99.2. 2026.

Miscellaneous databases

EvolutionaryTraceiP0A794.
PROiP0A794.

Family and domain databases

CDDicd00003. PNPsynthase. 1 hit.
Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00279. PdxJ. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR004569. PyrdxlP_synth_PdxJ.
[Graphical view]
PfamiPF03740. PdxJ. 1 hit.
[Graphical view]
SUPFAMiSSF63892. SSF63892. 1 hit.
TIGRFAMsiTIGR00559. pdxJ. 1 hit.
ProtoNetiSearch...

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 2, 2016
This is version 103 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

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 one 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.