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Protein

Pyridoxine 5'-phosphate synthase

Gene

pdxJ

Organism
Burkholderia pseudomallei (strain 1710b)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

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: 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), Phosphoserine aminotransferase (serC-2)
  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)DescriptionActionsGraphical viewLength
Binding sitei163-amino-2-oxopropyl phosphateUniRule annotation1
Binding sitei273-amino-2-oxopropyl phosphateUniRule annotation1
Active sitei52Proton acceptorUniRule annotation1
Binding sitei541-deoxy-D-xylulose 5-phosphateUniRule annotation1
Binding sitei591-deoxy-D-xylulose 5-phosphateUniRule annotation1
Active sitei79Proton acceptorUniRule annotation1
Binding sitei1091-deoxy-D-xylulose 5-phosphateUniRule annotation1
Sitei160Transition state stabilizerUniRule annotation1
Active sitei200Proton donorUniRule annotation1
Binding sitei2013-amino-2-oxopropyl phosphate; via amide nitrogenUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transferase

Keywords - Biological processi

Pyridoxine biosynthesis

Enzyme and pathway databases

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:BURPS1710b_2892
OrganismiBurkholderia pseudomallei (strain 1710b)
Taxonomic identifieri320372 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderiapseudomallei group
Proteomesi
  • UP000002700 Componenti: Chromosome I

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002317941 – 257Pyridoxine 5'-phosphate synthaseAdd BLAST257

Interactioni

Subunit structurei

Homooctamer; tetramer of dimers.UniRule annotation

Structurei

Secondary structure

1257
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi8 – 10Combined sources3
Beta strandi11 – 16Combined sources6
Helixi18 – 27Combined sources10
Beta strandi28 – 30Combined sources3
Helixi34 – 43Combined sources10
Beta strandi47 – 52Combined sources6
Beta strandi58 – 60Combined sources3
Helixi62 – 71Combined sources10
Beta strandi76 – 80Combined sources5
Helixi84 – 93Combined sources10
Beta strandi96 – 100Combined sources5
Helixi105 – 107Combined sources3
Beta strandi110 – 114Combined sources5
Turni116 – 119Combined sources4
Helixi120 – 132Combined sources13
Beta strandi136 – 141Combined sources6
Helixi145 – 154Combined sources10
Beta strandi157 – 161Combined sources5
Helixi164 – 167Combined sources4
Helixi172 – 191Combined sources20
Beta strandi195 – 198Combined sources4
Turni204 – 206Combined sources3
Helixi207 – 211Combined sources5
Beta strandi216 – 221Combined sources6
Helixi223 – 232Combined sources10
Helixi234 – 253Combined sources20

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3GK0X-ray2.28A/B/C/D/E/F/G/H1-257[»]
ProteinModelPortaliQ3JQ80.
SMRiQ3JQ80.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ3JQ80.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni18 – 191-deoxy-D-xylulose 5-phosphate bindingUniRule annotation2
Regioni222 – 2233-amino-2-oxopropyl phosphate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the PNP synthase family.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000258094.
KOiK03474.
OMAiERHIRYQ.

Family and domain databases

CDDicd00003. PNPsynthase. 1 hit.
Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00279. PdxJ. 1 hit.
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.

Q3JQ80-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSFFLTTPAA IDLGVNIDHV ATLRNARGTA YPDPVRAALA AEDAGADAIT
60 70 80 90 100
LHLREDRRHI VDADVRTLRP RVKTRMNLEC AVTPEMLDIA CEIRPHDACL
110 120 130 140 150
VPEKRSELTT EGGLDVVGHF DAVRAACKQL ADAGVRVSLF IDPDEAQIRA
160 170 180 190 200
AHETGAPVIE LHTGRYADAH DAAEQQREFE RIATGVDAGI ALGLKVNAGH
210 220 230 240 250
GLHYTNVQAI AALPGIAELN IGHAIVAHAV FVGWDNAVRE MKAIMVAARV

AALHGGR
Length:257
Mass (Da):27,509
Last modified:November 8, 2005 - v1
Checksum:iA4BD148BDA418247
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000124 Genomic DNA. Translation: ABA48208.1.
RefSeqiWP_004524619.1. NC_007434.1.

Genome annotation databases

EnsemblBacteriaiABA48208; ABA48208; BURPS1710b_2892.
KEGGibpm:BURPS1710b_2892.
PATRICi19238324. VBIBurPse115837_3021.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000124 Genomic DNA. Translation: ABA48208.1.
RefSeqiWP_004524619.1. NC_007434.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3GK0X-ray2.28A/B/C/D/E/F/G/H1-257[»]
ProteinModelPortaliQ3JQ80.
SMRiQ3JQ80.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABA48208; ABA48208; BURPS1710b_2892.
KEGGibpm:BURPS1710b_2892.
PATRICi19238324. VBIBurPse115837_3021.

Phylogenomic databases

HOGENOMiHOG000258094.
KOiK03474.
OMAiERHIRYQ.

Enzyme and pathway databases

UniPathwayiUPA00244; UER00313.

Miscellaneous databases

EvolutionaryTraceiQ3JQ80.

Family and domain databases

CDDicd00003. PNPsynthase. 1 hit.
Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00279. PdxJ. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR004569. PyrdxlP_synth_PdxJ.
[Graphical view]
PfamiPF03740. PdxJ. 1 hit.
[Graphical view]
SUPFAMiSSF63892. SSF63892. 1 hit.
TIGRFAMsiTIGR00559. pdxJ. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiPDXJ_BURP1
AccessioniPrimary (citable) accession number: Q3JQ80
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 4, 2006
Last sequence update: November 8, 2005
Last modified: November 2, 2016
This is version 74 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

3D-structure, Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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 one 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.