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Protein

Pyridoxine 5'-phosphate synthase

Gene

pdxJ

Organism
Helicobacter pylori (strain HPAG1)
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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei6 – 613-amino-2-oxopropyl phosphateUniRule annotation
Binding sitei17 – 1713-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 sitei102 – 10211-deoxy-D-xylulose 5-phosphateUniRule annotation
Sitei151 – 1511Transition state stabilizerUniRule annotation
Active sitei215 – 2151Proton donorUniRule annotation
Binding sitei216 – 21613-amino-2-oxopropyl phosphate; via amide nitrogenUniRule annotation

GO - Molecular functioni

  1. pyridoxine 5'-phosphate synthase activity Source: UniProtKB-EC

GO - Biological processi

  1. pyridoxine biosynthetic process Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Pyridoxine biosynthesis

Enzyme and pathway databases

BioCyciHPYL357544:GH1F-1568-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:HPAG1_1530
OrganismiHelicobacter pylori (strain HPAG1)
Taxonomic identifieri357544 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
ProteomesiUP000008835 Componenti: Chromosome

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 262262Pyridoxine 5'-phosphate synthasePRO_1000022375Add
BLAST

Interactioni

Subunit structurei

Homooctamer; tetramer of dimers.UniRule annotation

Protein-protein interaction databases

STRINGi357544.HPAG1_1530.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni8 – 921-deoxy-D-xylulose 5-phosphate bindingUniRule annotation
Regioni237 – 23823-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.

Q1CR25-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRFGLNIDHI VTLREIRKTY EPEILEALFI AKNTHKVDLI TIHLREDKRH
60 70 80 90 100
IQNEDVLRLL EISPLPINIE CSINVAITDF LCSLKNKPSK VTIVPENRNE
110 120 130 140 150
VTTEGGLDCS LKGLGEVIRA YHNKGIEVSL FVDPLKDALH FAKEHQVKQV
160 170 180 190 200
EFHTGVYANL HNALYSNANN QIHAISALKD KCPKELKEEL HNAFLQLRRM
210 220 230 240 250
SKEAFFMGIV VCAGHGLNYT NVKELLKIPS LRELNIGHSV VSKAVLVGLE
260
KAILEMAQLI KR
Length:262
Mass (Da):29,663
Last modified:July 11, 2006 - v1
Checksum:iCFC43A73505EC354
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000241 Genomic DNA. Translation: ABF85597.1.
RefSeqiYP_628271.1. NC_008086.1.

Genome annotation databases

EnsemblBacteriaiABF85597; ABF85597; HPAG1_1530.
KEGGihpa:HPAG1_1530.
PATRICi20604533. VBIHelPyl56048_1585.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000241 Genomic DNA. Translation: ABF85597.1.
RefSeqiYP_628271.1. NC_008086.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi357544.HPAG1_1530.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABF85597; ABF85597; HPAG1_1530.
KEGGihpa:HPAG1_1530.
PATRICi20604533. VBIHelPyl56048_1585.

Phylogenomic databases

eggNOGiCOG0854.
HOGENOMiHOG000258094.
KOiK03474.
OMAiGMEELNI.
OrthoDBiEOG6M9F0H.

Enzyme and pathway databases

UniPathwayiUPA00244; UER00313.
BioCyciHPYL357544:GH1F-1568-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. "The complete genome sequence of a chronic atrophic gastritis Helicobacter pylori strain: evolution during disease progression."
    Oh J.D., Kling-Baeckhed H., Giannakis M., Xu J., Fulton R.S., Fulton L.A., Cordum H.S., Wang C., Elliott G., Edwards J., Mardis E.R., Engstrand L.G., Gordon J.I.
    Proc. Natl. Acad. Sci. U.S.A. 103:9999-10004(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: HPAG1.

Entry informationi

Entry nameiPDXJ_HELPH
AccessioniPrimary (citable) accession number: Q1CR25
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 15, 2008
Last sequence update: July 11, 2006
Last modified: April 1, 2015
This is version 60 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

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.