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A5VD52 (A5VD52_SPHWW) Unreviewed, UniProtKB/TrEMBL

Last modified May 1, 2013. Version 46. 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:Swit_3873 EMBL ABQ70218.1
OrganismSphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273) [Complete proteome] [HAMAP] EMBL ABQ70218.1
Taxonomic identifier392499 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Alphaproteobacteria › Sphingomonadales › Sphingomonadaceae › Sphingomonas ›

Protein attributes

Sequence length241 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
Region214 – 21523-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 site1921Proton 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 site19313-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
A5VD52 [UniParc].

Last modified July 10, 2007. Version 1.
Checksum: 7E9C0043F613576A

FASTA24126,087
        10         20         30         40         50         60 
MSRLRLGVNI DHVATIRNAR GGLHPDPIRA AEIASEAGAD GITAHLREDR RHIMDDDIGR 

        70         80         90        100        110        120 
LIGGIALPIN LEMAATEEML AIALRHRPHA ACIVPERREE VTTEGGLDAA GQHNHLKPLI 

       130        140        150        160        170        180 
AKLSDAGIRV SLFIEPTPRQ IEAAVSLRAP VVEFHTGRYA HAEGEERATE LRRIADAAAL 

       190        200        210        220        230        240 
AAKNGIEPHA GHGLTFDNVV PIAAIPQIAE LNIGHFLIGE AIFDGLAPVV RRMRQLMDEA 


R

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References

[1]"Complete sequence of chromosome of Sphingomonas wittichii RW1."
US DOE Joint Genome Institute
Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E., Tice H., Pitluck S., Saunders E., Brettin T., Bruce D., Detter J.C., Han C., Tapia R., Gilna P., Schmutz J., Larimer F., Land M. expand/collapse author list , Hauser L., Kyrpides N., Kim E., Halden R.U., Miller T.R., Salzberg S.L., Eisen J.A., Richardson P.
Submitted (MAY-2007) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: RW1 / DSM 6014 / JCM 10273.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP000699 Genomic DNA. Translation: ABQ70218.1.
RefSeqYP_001264356.1. NC_009511.1.

3D structure databases

ProteinModelPortalA5VD52.
SMRA5VD52. Positions 2-241.
ModBaseSearch...

Protein-protein interaction databases

STRING392499.Swit_3873.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABQ70218; ABQ70218; Swit_3873.
GeneID5197593.
KEGGswi:Swit_3873.
PATRIC23687015. VBISphWit55028_4439.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0854.
HOGENOMHOG000258094.
KOK03474.
OMALHYHNVK.
ProtClustDBPRK05265.

Enzyme and pathway databases

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 nameA5VD52_SPHWW
AccessionPrimary (citable) accession number: A5VD52
Entry history
Integrated into UniProtKB/TrEMBL: July 10, 2007
Last sequence update: July 10, 2007
Last modified: May 1, 2013
This is version 46 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