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Protein

Pyridoxine 5'-phosphate synthase

Gene

pdxJ

Organism
Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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.UniRule annotation

Catalytic activityi

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

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.UniRule annotation
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. D-erythrose-4-phosphate dehydrogenase (Pput_4837)
  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 sitei63-amino-2-oxopropyl phosphateUniRule annotation1
Binding sitei173-amino-2-oxopropyl phosphateUniRule annotation1
Active sitei42Proton acceptorUniRule annotation1
Binding sitei441-deoxy-D-xylulose 5-phosphateUniRule annotation1
Binding sitei491-deoxy-D-xylulose 5-phosphateUniRule annotation1
Active sitei69Proton acceptorUniRule annotation1
Binding sitei991-deoxy-D-xylulose 5-phosphateUniRule annotation1
Sitei150Transition state stabilizerUniRule annotation1
Active sitei190Proton donorUniRule annotation1
Binding sitei1913-amino-2-oxopropyl phosphate; via amide nitrogenUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Pyridoxine biosynthesis

Enzyme and pathway databases

UniPathwayiUPA00244; UER00313.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxine 5'-phosphate synthaseUniRule annotation (EC:2.6.99.2UniRule annotation)
Short name:
PNP synthaseUniRule annotation
Gene namesi
Name:pdxJUniRule annotation
Ordered Locus Names:Pput_4285
OrganismiPseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1)
Taxonomic identifieri351746 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
Proteomesi
  • UP000006553 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_10000223941 – 240Pyridoxine 5'-phosphate synthaseAdd BLAST240

Interactioni

Subunit structurei

Homooctamer; tetramer of dimers.UniRule annotation

Protein-protein interaction databases

STRINGi351746.Pput_4285.

Structurei

3D structure databases

ProteinModelPortaliA5W8E9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni8 – 91-deoxy-D-xylulose 5-phosphate bindingUniRule annotation2
Regioni212 – 2133-amino-2-oxopropyl phosphate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the PNP synthase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CSZ. Bacteria.
COG0854. LUCA.
HOGENOMiHOG000258094.
KOiK03474.
OMAiERHIRYQ.

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.

A5W8E9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLLGVNIDHV ATLRQARGTR YPDPVKAALD AEEAGADGIT VHLREDRRHI
60 70 80 90 100
QERDVVLLKD VLQTRMNFEM GVTEEMMAFA EKIRPAHICL VPETRQELTT
110 120 130 140 150
EGGLDVAGQE ARIKAAVERL ARTGAEVSLF IDADERQIEA SRRVGAPAIE
160 170 180 190 200
LHTGRYADAE TPTEVAEELQ RIVEGVAFGV GHGLIVNAGH GLHYHNVEAV
210 220 230 240
AAIKGINELN IGHALVAHAL FVGFKAAVAE MKALIVAASR
Length:240
Mass (Da):26,011
Last modified:July 10, 2007 - v1
Checksum:i1CE1D4DA55E9D84F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000712 Genomic DNA. Translation: ABQ80409.1.

Genome annotation databases

EnsemblBacteriaiABQ80409; ABQ80409; Pput_4285.
KEGGippf:Pput_4285.
PATRICi19924785. VBIPsePut56420_4343.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000712 Genomic DNA. Translation: ABQ80409.1.

3D structure databases

ProteinModelPortaliA5W8E9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi351746.Pput_4285.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABQ80409; ABQ80409; Pput_4285.
KEGGippf:Pput_4285.
PATRICi19924785. VBIPsePut56420_4343.

Phylogenomic databases

eggNOGiENOG4105CSZ. Bacteria.
COG0854. LUCA.
HOGENOMiHOG000258094.
KOiK03474.
OMAiERHIRYQ.

Enzyme and pathway databases

UniPathwayiUPA00244; UER00313.

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_PSEP1
AccessioniPrimary (citable) accession number: A5W8E9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: July 10, 2007
Last modified: November 2, 2016
This is version 59 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.