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Protein

Pyridoxine 5'-phosphate synthase

Gene

pdxJ

Organism
Yersinia pestis
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. D-erythrose-4-phosphate dehydrogenase (epd), D-erythrose-4-phosphate dehydrogenase (gapA)
  2. Erythronate-4-phosphate dehydrogenase (pdxB)
  3. Phosphoserine aminotransferase (serC), Phosphoserine aminotransferase (serC)
  4. 4-hydroxythreonine-4-phosphate dehydrogenase (pdxA), 4-hydroxythreonine-4-phosphate dehydrogenase (pdxA)
  5. Pyridoxine 5'-phosphate synthase (pdxJ), 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 sitei93-amino-2-oxopropyl phosphateUniRule annotation1
Binding sitei203-amino-2-oxopropyl phosphateUniRule annotation1
Active sitei45Proton acceptorUniRule annotation1
Binding sitei471-deoxy-D-xylulose 5-phosphateUniRule annotation1
Binding sitei521-deoxy-D-xylulose 5-phosphateUniRule annotation1
Active sitei72Proton acceptorUniRule annotation1
Binding sitei1021-deoxy-D-xylulose 5-phosphateUniRule annotation1
Sitei153Transition state stabilizerUniRule annotation1
Active sitei193Proton donorUniRule annotation1
Binding sitei1943-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:YPO2930, y1300, YP_2525
OrganismiYersinia pestis
Taxonomic identifieri632 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesYersiniaceaeYersinia
Proteomesi
  • UP000000815 Componenti: Chromosome
  • UP000001019 Componenti: Chromosome
  • UP000002490 Componenti: Chromosome

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_00001901441 – 243Pyridoxine 5'-phosphate synthaseAdd BLAST243

Proteomic databases

PRIDEiQ8ZCP4.

Interactioni

Subunit structurei

Homooctamer; tetramer of dimers.UniRule annotation

Protein-protein interaction databases

IntActiQ8ZCP4. 1 interactor.
STRINGi187410.y1300.

Structurei

Secondary structure

1243
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi5 – 9Combined sources5
Helixi11 – 18Combined sources8
Turni19 – 21Combined sources3
Helixi27 – 36Combined sources10
Beta strandi40 – 45Combined sources6
Beta strandi51 – 53Combined sources3
Helixi55 – 64Combined sources10
Beta strandi69 – 75Combined sources7
Helixi77 – 86Combined sources10
Beta strandi89 – 94Combined sources6
Helixi98 – 100Combined sources3
Beta strandi105 – 107Combined sources3
Helixi110 – 112Combined sources3
Helixi113 – 124Combined sources12
Turni125 – 127Combined sources3
Beta strandi129 – 134Combined sources6
Helixi138 – 146Combined sources9
Beta strandi150 – 155Combined sources6
Helixi157 – 161Combined sources5
Helixi165 – 184Combined sources20
Beta strandi188 – 194Combined sources7
Turni197 – 199Combined sources3
Helixi200 – 205Combined sources6
Beta strandi209 – 214Combined sources6
Helixi216 – 225Combined sources10
Helixi227 – 241Combined sources15

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3F4NX-ray2.40A/B/C/D/E/F/G/H1-243[»]
ProteinModelPortaliQ8ZCP4.
SMRiQ8ZCP4.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8ZCP4.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni11 – 121-deoxy-D-xylulose 5-phosphate bindingUniRule annotation2
Regioni215 – 2163-amino-2-oxopropyl phosphate bindingUniRule annotation2

Sequence similaritiesi

Belongs to the PNP synthase family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CSZ. Bacteria.
COG0854. LUCA.
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.

Q8ZCP4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MADLLLGVNI DHIATLRNAR GTIYPDPVQA AFIAEQAGAD GITVHLREDR
60 70 80 90 100
RHITDRDVRI LRQTIQTRMN LEMAVTDEMV DIACDIKPHF CCLVPEKRQE
110 120 130 140 150
VTTEGGLDVA GQVDKMTLAV GRLADVGILV SLFIDADFRQ IDAAVAAGAP
160 170 180 190 200
YIEIHTGAYA DASTVLERQA ELMRIAKAAT YAAGKGLKVN AGHGLTYHNV
210 220 230 240
QPIAALPEMH ELNIGHAIIG QAVMTGLAAA VTDMKVLMRE ARR
Length:243
Mass (Da):26,297
Last modified:March 5, 2002 - v1
Checksum:i0C369688908E0758
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL21538.1.
AE009952 Genomic DNA. Translation: AAM84874.1.
AE017042 Genomic DNA. Translation: AAS62723.1.
PIRiAG0356.
RefSeqiWP_002211569.1. NZ_LQBA01000004.1.
YP_002347860.1. NC_003143.1.

Genome annotation databases

EnsemblBacteriaiAAM84874; AAM84874; y1300.
AAS62723; AAS62723; YP_2525.
GeneIDi1175751.
KEGGiype:YPO2930.
ypk:y1300.
ypm:YP_2525.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL590842 Genomic DNA. Translation: CAL21538.1.
AE009952 Genomic DNA. Translation: AAM84874.1.
AE017042 Genomic DNA. Translation: AAS62723.1.
PIRiAG0356.
RefSeqiWP_002211569.1. NZ_LQBA01000004.1.
YP_002347860.1. NC_003143.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3F4NX-ray2.40A/B/C/D/E/F/G/H1-243[»]
ProteinModelPortaliQ8ZCP4.
SMRiQ8ZCP4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ8ZCP4. 1 interactor.
STRINGi187410.y1300.

Proteomic databases

PRIDEiQ8ZCP4.

Protocols and materials databases

DNASUi1146247.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAM84874; AAM84874; y1300.
AAS62723; AAS62723; YP_2525.
GeneIDi1175751.
KEGGiype:YPO2930.
ypk:y1300.
ypm:YP_2525.

Phylogenomic databases

eggNOGiENOG4105CSZ. Bacteria.
COG0854. LUCA.
HOGENOMiHOG000258094.
KOiK03474.
OMAiERHIRYQ.

Enzyme and pathway databases

UniPathwayiUPA00244; UER00313.

Miscellaneous databases

EvolutionaryTraceiQ8ZCP4.

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_YERPE
AccessioniPrimary (citable) accession number: Q8ZCP4
Secondary accession number(s): Q0WCX8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 5, 2002
Last sequence update: March 5, 2002
Last modified: November 2, 2016
This is version 108 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, Reference 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.