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Protein

Pyridoxine 5'-phosphate synthase

Gene

pdxJ

Organism
Magnetococcus sp. (strain MC-1)
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: 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. no protein annotated in this organism
  2. no protein annotated in this organism
  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 sitei7 – 713-amino-2-oxopropyl phosphateUniRule annotation
Binding sitei18 – 1813-amino-2-oxopropyl phosphateUniRule annotation
Active sitei43 – 431Proton acceptorUniRule annotation
Binding sitei45 – 4511-deoxy-D-xylulose 5-phosphateUniRule annotation
Binding sitei50 – 5011-deoxy-D-xylulose 5-phosphateUniRule annotation
Active sitei70 – 701Proton acceptorUniRule annotation
Binding sitei100 – 10011-deoxy-D-xylulose 5-phosphateUniRule annotation
Sitei151 – 1511Transition state stabilizerUniRule annotation
Active sitei191 – 1911Proton donorUniRule annotation
Binding sitei192 – 19213-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

BioCyciMSP156889:GH36-1879-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:Mmc1_1860
OrganismiMagnetococcus sp. (strain MC-1)
Taxonomic identifieri156889 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaMagnetococcalesMagnetococcaceaeMagnetococcus
ProteomesiUP000002586 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 – 243243Pyridoxine 5'-phosphate synthasePRO_1000022378Add
BLAST

Interactioni

Subunit structurei

Homooctamer; tetramer of dimers.UniRule annotation

Protein-protein interaction databases

STRINGi156889.Mmc1_1860.

Structurei

3D structure databases

ProteinModelPortaliA0L8S5.
SMRiA0L8S5. Positions 2-239.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni9 – 1021-deoxy-D-xylulose 5-phosphate bindingUniRule annotation
Regioni213 – 21423-amino-2-oxopropyl phosphate bindingUniRule annotation

Sequence similaritiesi

Belongs to the PNP synthase family.UniRule annotation

Phylogenomic databases

eggNOGiCOG0854.
HOGENOMiHOG000258095.
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.

A0L8S5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MILLGVNIDH IATLRQARGE RYPDPVDAAF AAERAGADSI TVHLREDRRH
60 70 80 90 100
IQDRDVVLLQ QTCQTKINLE MAASEPMLTL AERWKPQDCC LVPEKRHELT
110 120 130 140 150
TEGGLDVVGN RHRLADAVAR LHDAGIRVSL FVDPDLEQIS AAGAIGATVV
160 170 180 190 200
EMHTGRYANA ATQAQRNLEL EQLYRAAHQA SLNGLTVHAG HGLTYHNVQP
210 220 230 240
IARLPDLKEL NIGHAIIARA VMVGMESAVK EMKRLMREAV KTP
Length:243
Mass (Da):26,799
Last modified:December 12, 2006 - v1
Checksum:i6B275C2FAD05E5D5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000471 Genomic DNA. Translation: ABK44368.1.
RefSeqiWP_011713512.1. NC_008576.1.
YP_865774.1. NC_008576.1.

Genome annotation databases

EnsemblBacteriaiABK44368; ABK44368; Mmc1_1860.
KEGGimgm:Mmc1_1860.
PATRICi22430309. VBIMagSp23654_1909.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000471 Genomic DNA. Translation: ABK44368.1.
RefSeqiWP_011713512.1. NC_008576.1.
YP_865774.1. NC_008576.1.

3D structure databases

ProteinModelPortaliA0L8S5.
SMRiA0L8S5. Positions 2-239.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi156889.Mmc1_1860.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABK44368; ABK44368; Mmc1_1860.
KEGGimgm:Mmc1_1860.
PATRICi22430309. VBIMagSp23654_1909.

Phylogenomic databases

eggNOGiCOG0854.
HOGENOMiHOG000258095.
KOiK03474.
OMAiGMEELNI.
OrthoDBiEOG6M9F0H.

Enzyme and pathway databases

UniPathwayiUPA00244; UER00313.
BioCyciMSP156889:GH36-1879-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: MC-1.

Entry informationi

Entry nameiPDXJ_MAGSM
AccessioniPrimary (citable) accession number: A0L8S5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: December 12, 2006
Last modified: May 27, 2015
This is version 53 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.