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Protein

Pyridoxal 5'-phosphate synthase subunit PDX1

Gene

PDX1

Organism
Phaseolus vulgaris (Kidney bean) (French bean)
Status
Reviewed-Annotation score: -Experimental evidence at transcript leveli

Functioni

Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by PDX2. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively. Also plays an indirect role in resistance to singlet oxygen-generating photosensitizers.By similarity

Miscellaneous

Vitamin B6 is an essential quencher of singlet oxygen in plants, that can protect cellular membranes from lipid peroxidation.

Catalytic activityi

D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate.By similarity

Pathwayi: pyridoxal 5'-phosphate biosynthesis

This protein is involved in the pathway pyridoxal 5'-phosphate biosynthesis, which is part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the pathway pyridoxal 5'-phosphate biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei43D-ribose 5-phosphateBy similarity1
Active sitei100Schiff-base intermediate with D-ribose 5-phosphateBy similarity1
Binding sitei172D-ribose 5-phosphate; via amide nitrogenBy similarity1
Binding sitei184Glyceraldehyde 3-phosphateBy similarity1
Binding sitei233D-ribose 5-phosphate; via amide nitrogenBy similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLyase
LigandPyridoxal phosphate, Schiff base

Enzyme and pathway databases

UniPathwayiUPA00245

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxal 5'-phosphate synthase subunit PDX1 (EC:4.3.3.6)
Short name:
PLP synthase subunit PDX1
Alternative name(s):
pvPDX1
Gene namesi
Name:PDX1
OrganismiPhaseolus vulgaris (Kidney bean) (French bean)
Taxonomic identifieri3885 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsfabidsFabalesFabaceaePapilionoideaePhaseoleaePhaseolus

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001093721 – 312Pyridoxal 5'-phosphate synthase subunit PDX1Add BLAST312

Expressioni

Inductioni

By wounding, gibberelic acid and 1-aminocyclopropane-1-carboxylic acid (ACC), but not after treatment with methyl jasmonate or active oxygen species.1 Publication

Interactioni

GO - Molecular functioni

Structurei

3D structure databases

ProteinModelPortaliQ9FT25
SMRiQ9FT25
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni254 – 255D-ribose 5-phosphate bindingBy similarity2

Sequence similaritiesi

Belongs to the PdxS/SNZ family.Curated

Phylogenomic databases

KOiK06215
PhylomeDBiQ9FT25

Family and domain databases

CDDicd04727 pdxS, 1 hit
Gene3Di3.20.20.70, 1 hit
HAMAPiMF_01824 PdxS, 1 hit
InterProiView protein in InterPro
IPR013785 Aldolase_TIM
IPR001852 PdxS/SNZ
IPR033755 PdxS/SNZ_N
IPR011060 RibuloseP-bd_barrel
PANTHERiPTHR31829 PTHR31829, 1 hit
PfamiView protein in Pfam
PF01680 SOR_SNZ, 1 hit
PIRSFiPIRSF029271 Pdx1, 1 hit
SUPFAMiSSF51366 SSF51366, 1 hit
TIGRFAMsiTIGR00343 TIGR00343, 1 hit
PROSITEiView protein in PROSITE
PS01235 PDXS_SNZ_1, 1 hit
PS51129 PDXS_SNZ_2, 1 hit

Sequencei

Sequence statusi: Complete.

Q9FT25-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEGEGSRVVA LYDGNGAITE TKKSPFSVKV GLAQMLRGGV IMDVVNADQA
60 70 80 90 100
RIAEEAGACA VMALERVPAD IRAQGGVARM SDPQLIKEIK RAVTIPVMAK
110 120 130 140 150
ARIGHFVEAQ ILEAIGIDYV DESEVLTLAD DANHINKHNF RIPFVCGCRN
160 170 180 190 200
LGEALRRIRE GAAMIRTKGE AGTGNIIEAV RHVRSVMSDI RVLRNMDDDE
210 220 230 240 250
VFTFAKSIAA PYDLVMQTKQ LGRLPVVHFA AGGVATPADA ALMMQLGCDG
260 270 280 290 300
VFVGSGVFKS GDPAKRARAI VQAVTHYSDP EILAEVSCGL GEAMVGINLS
310
DTNVERFANR SE
Length:312
Mass (Da):33,405
Last modified:March 1, 2001 - v1
Checksum:iEF614F045AB959C2
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY007525 mRNA Translation: AAG17942.1
RefSeqiXP_007147987.1, XM_007147925.1

Genome annotation databases

EnsemblPlantsiESW19981; ESW19981; PHAVU_006G171100g
GeneIDi18629076
GrameneiESW19981; ESW19981; PHAVU_006G171100g
KEGGipvu:PHAVU_006G171100g

Similar proteinsi

Entry informationi

Entry nameiPDX1_PHAVU
AccessioniPrimary (citable) accession number: Q9FT25
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 15, 2004
Last sequence update: March 1, 2001
Last modified: February 28, 2018
This is version 73 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

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