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D0JN40 (D0JN40_YERP1) Unreviewed, UniProtKB/TrEMBL

Last modified May 29, 2013. Version 24. 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 EMBL ACY63058.1
Ordered Locus Names:YPD8_2383 EMBL ACY63058.1
OrganismYersinia pestis (strain D182038) [Complete proteome] [HAMAP] EMBL ACY63058.1
Taxonomic identifier637385 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Yersinia ›

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
D0JN40 [UniParc].

Last modified December 15, 2009. Version 1.
Checksum: 0C369688908E0758

FASTA24326,297
        10         20         30         40         50         60 
MADLLLGVNI DHIATLRNAR GTIYPDPVQA AFIAEQAGAD GITVHLREDR RHITDRDVRI 

        70         80         90        100        110        120 
LRQTIQTRMN LEMAVTDEMV DIACDIKPHF CCLVPEKRQE VTTEGGLDVA GQVDKMTLAV 

       130        140        150        160        170        180 
GRLADVGILV SLFIDADFRQ IDAAVAAGAP YIEIHTGAYA DASTVLERQA ELMRIAKAAT 

       190        200        210        220        230        240 
YAAGKGLKVN AGHGLTYHNV QPIAALPEMH ELNIGHAIIG QAVMTGLAAA VTDMKVLMRE 


ARR

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References

[1]"Spatial variation of Yersinia pestis from Yunnan Province of China."
Zhang Z., Hai R., Song Z., Xia L., Liang Y., Cai H., Liang Y., Shen X., Zhang E., Xu J., Yu D., Yu X.J.
Am. J. Trop. Med. Hyg. 81:714-717(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: D182038 EMBL ACY63058.1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP001589 Genomic DNA. Translation: ACY63058.1.
RefSeqYP_005509451.1. NC_017160.1.

3D structure databases

ProteinModelPortalD0JN40.
SMRD0JN40. Positions 2-242.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACY63058; ACY63058; YPD8_2383.
GeneID12097316.
KEGGypx:YPD8_2383.
PATRIC36769340. VBIYerPes93679_3181.

Organism-specific databases

CMRSearch...

Phylogenomic databases

KOK03474.
OMALHYHNVK.

Enzyme and pathway databases

BioCycYPES637385:GLMY-2419-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 nameD0JN40_YERP1
AccessionPrimary (citable) accession number: D0JN40
Entry history
Integrated into UniProtKB/TrEMBL: December 15, 2009
Last sequence update: December 15, 2009
Last modified: May 29, 2013
This is version 24 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)
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