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F7YLM6 (F7YLM6_VIBA7) Unreviewed, UniProtKB/TrEMBL

Last modified April 3, 2013. Version 12. Feed History...

Clusters with 100%, 90%, 50% identity | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Pyridoxine 5'-phosphate synthase HAMAP-Rule MF_00279
Short name=PNP synthase HAMAP-Rule MF_00279
EC=2.6.99.2 HAMAP-Rule MF_00279
Gene names
Name:pdxJ HAMAP-Rule MF_00279
Ordered Locus Names:VAA_03772 EMBL AEH32325.1
OrganismVibrio anguillarum (strain ATCC 68554 / 775) (Listonella anguillarum) [Complete proteome] [HAMAP] EMBL AEH32325.1
Taxonomic identifier882102 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio ›

Protein attributes

Sequence length243 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

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 By similarity. HAMAP-Rule MF_00279 SAAS SAAS004569

Catalytic activity

1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H2O. HAMAP-Rule MF_00279 SAAS SAAS004569

Pathway

Cofactor biosynthesis; pyridoxine 5'-phosphate biosynthesis; pyridoxine 5'-phosphate from D-erythrose 4-phosphate: step 5/5. HAMAP-Rule MF_00279 SAAS SAAS004569

Subunit structure

Homooctamer; tetramer of dimers By similarity. HAMAP-Rule MF_00279 SAAS SAAS004569

Subcellular location

Cytoplasm By similarity HAMAP-Rule MF_00279 SAAS SAAS004569.

Sequence similarities

Belongs to the PNP synthase family. HAMAP-Rule MF_00279

Ontologies

Keywords
   Biological processPyridoxine biosynthesis HAMAP-Rule MF_00279 SAAS SAAS004569
   Cellular componentCytoplasm HAMAP-Rule MF_00279 SAAS SAAS004569
   Molecular functionTransferase HAMAP-Rule MF_00279 SAAS SAAS004569
   Technical termComplete proteome
Gene Ontology (GO)
   Biological_processpyridoxine biosynthetic process

Inferred from electronic annotation. Source: HAMAP

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionpyridoxine 5'-phosphate synthase activity

Inferred from electronic annotation. Source: EC

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Regions

Region11 – 1221-deoxy-D-xylulose 5-phosphate binding By similarity HAMAP-Rule MF_00279
Region215 – 21623-amino-2-oxopropyl phosphate binding By similarity HAMAP-Rule MF_00279

Sites

Active site451Proton acceptor By similarity HAMAP-Rule MF_00279
Active site721Proton acceptor By similarity HAMAP-Rule MF_00279
Active site1931Proton donor By similarity HAMAP-Rule MF_00279
Binding site913-amino-2-oxopropyl phosphate By similarity HAMAP-Rule MF_00279
Binding site2013-amino-2-oxopropyl phosphate By similarity HAMAP-Rule MF_00279
Binding site4711-deoxy-D-xylulose 5-phosphate By similarity HAMAP-Rule MF_00279
Binding site5211-deoxy-D-xylulose 5-phosphate By similarity HAMAP-Rule MF_00279
Binding site10211-deoxy-D-xylulose 5-phosphate By similarity HAMAP-Rule MF_00279
Binding site19413-amino-2-oxopropyl phosphate; via amide nitrogen By similarity HAMAP-Rule MF_00279
Site1531Transition state stabilizer By similarity HAMAP-Rule MF_00279

Sequences

Sequence LengthMass (Da)Tools
F7YLM6 [UniParc].

Last modified September 21, 2011. Version 1.
Checksum: 833FD75A0783E53B

FASTA24326,483
        10         20         30         40         50         60 
MSAIYLGVNI DHIATLRNAR GTKYPDPVHA AEMAERAGAD GITIHLREDR RHIKDRDVRI 

        70         80         90        100        110        120 
LRETLQTRMN LEMAVTDEMI DIALQTQPEF VCLVPEKREE LTTEGGLDVL GQLDKVKAAT 

       130        140        150        160        170        180 
EKLTAAGIKV SLFIDADREQ INAAKTCGAP FIELHTGHYA DATTEADQQD ELKKIAAAAS 

       190        200        210        220        230        240 
YASDLGITVN AGHGLTYHNV AAIAALPEIY ELNIGHSIIG RAVFDGLEKS VADMKAIMQA 


ARK

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References

[1]"Complete genome sequence of the marine fish pathogen Vibrio anguillarum harboring the pJM1 virulence plasmid and genomic comparison with other virulent strains of V. anguillarum and V. ordalii."
Naka H., Dias G.M., Thompson C.C., Dubay C., Thompson F.L., Crosa J.H.
Infect. Immun. 79:2889-2900(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 68554 / 775.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP002284 Genomic DNA. Translation: AEH32325.1.
RefSeqYP_004565367.1. NC_015633.1.

3D structure databases

ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAEH32325; AEH32325; VAA_03772.
GeneID10774544.
KEGGvan:VAA_03772.

Organism-specific databases

CMRSearch...

Phylogenomic databases

KOK03474.

Enzyme and pathway databases

BioCycLANG882102:GIWG-765-MONOMER.
UniPathwayUPA00244; UER00313.

Family and domain databases

Gene3D3.20.20.70. 1 hit.
HAMAPMF_00279. PdxJ.
InterProIPR013785. Aldolase_TIM.
IPR004569. PyrdxlP_synth_PdxJ.
[Graphical view]
PfamPF03740. PdxJ. 1 hit.
[Graphical view]
SUPFAMSSF63892. PyrdxlP_synth_PdxJ. 1 hit.
TIGRFAMsTIGR00559. pdxJ. 1 hit.
ProtoNetSearch...

Entry information

Entry nameF7YLM6_VIBA7
AccessionPrimary (citable) accession number: F7YLM6
Entry history
Integrated into UniProtKB/TrEMBL: September 21, 2011
Last sequence update: September 21, 2011
Last modified: April 3, 2013
This is version 12 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info