Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Pyridoxine 5'-phosphate synthase

Gene

pdxJ

Organism
Alcanivorax borkumensis (strain ATCC 700651 / DSM 11573 / NCIMB 13689 / SK2)
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

Pathway:ipyridoxine 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. no protein annotated in this organism
  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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei12 – 1213-amino-2-oxopropyl phosphateUniRule annotation
Binding sitei23 – 2313-amino-2-oxopropyl phosphateUniRule annotation
Active sitei48 – 481Proton acceptorUniRule annotation
Binding sitei50 – 5011-deoxy-D-xylulose 5-phosphateUniRule annotation
Binding sitei55 – 5511-deoxy-D-xylulose 5-phosphateUniRule annotation
Active sitei75 – 751Proton acceptorUniRule annotation
Binding sitei105 – 10511-deoxy-D-xylulose 5-phosphateUniRule annotation
Sitei156 – 1561Transition state stabilizerUniRule annotation
Active sitei196 – 1961Proton donorUniRule annotation
Binding sitei197 – 19713-amino-2-oxopropyl phosphate; via amide nitrogenUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Pyridoxine biosynthesis

Enzyme and pathway databases

BioCyciABOR393595:GHRI-1668-MONOMER.
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:ABO_1628
OrganismiAlcanivorax borkumensis (strain ATCC 700651 / DSM 11573 / NCIMB 13689 / SK2)
Taxonomic identifieri393595 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaOceanospirillalesAlcanivoracaceaeAlcanivorax
ProteomesiUP000008871 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 244244Pyridoxine 5'-phosphate synthasePRO_1000059228Add
BLAST

Interactioni

Subunit structurei

Homooctamer; tetramer of dimers.UniRule annotation

Protein-protein interaction databases

STRINGi393595.ABO_1628.

Structurei

3D structure databases

ProteinModelPortaliQ0VP22.
SMRiQ0VP22. Positions 5-241.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni14 – 1521-deoxy-D-xylulose 5-phosphate bindingUniRule annotation
Regioni218 – 21923-amino-2-oxopropyl phosphate bindingUniRule annotation

Sequence similaritiesi

Belongs to the PNP synthase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0854.
HOGENOMiHOG000258094.
KOiK03474.
OMAiGMEELNI.
OrthoDBiEOG6M9F0H.

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.

Q0VP22-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSFMSRVLLG VNIDHIATLR QARGTRYPEP VQAALVAEQA GADGITVHLR
60 70 80 90 100
EDRRHINDRD VELLAQTLQT RMNLEMAATE EMVVIACRIQ PPHCCLVPEK
110 120 130 140 150
REELTTEGGL DVVGNKAWIA QCCQRLGQAG IEVSLFIDAE ESQILAAREC
160 170 180 190 200
GAPAIEIHTG GYADAQTIDQ QQQELARIRS AVAFALAQGL IVNAGHGLHY
210 220 230 240
HNTLAIAEIP GINELNIGHS IIARAAITGL DEAVRSMRSL LDTV
Length:244
Mass (Da):26,509
Last modified:September 5, 2006 - v1
Checksum:iCC67C57A7AED532B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM286690 Genomic DNA. Translation: CAL17076.1.

Genome annotation databases

EnsemblBacteriaiCAL17076; CAL17076; ABO_1628.
KEGGiabo:ABO_1628.
PATRICi20841055. VBIAlcBor124741_1705.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AM286690 Genomic DNA. Translation: CAL17076.1.

3D structure databases

ProteinModelPortaliQ0VP22.
SMRiQ0VP22. Positions 5-241.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi393595.ABO_1628.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAL17076; CAL17076; ABO_1628.
KEGGiabo:ABO_1628.
PATRICi20841055. VBIAlcBor124741_1705.

Phylogenomic databases

eggNOGiCOG0854.
HOGENOMiHOG000258094.
KOiK03474.
OMAiGMEELNI.
OrthoDBiEOG6M9F0H.

Enzyme and pathway databases

UniPathwayiUPA00244; UER00313.
BioCyciABOR393595:GHRI-1668-MONOMER.

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.
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700651 / DSM 11573 / NCIMB 13689 / SK2.

Entry informationi

Entry nameiPDXJ_ALCBS
AccessioniPrimary (citable) accession number: Q0VP22
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 5, 2008
Last sequence update: September 5, 2006
Last modified: July 22, 2015
This is version 63 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, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.