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Protein

Probable pyridoxal 5'-phosphate synthase subunit PDX1

Gene

PDX1

Organism
Ginkgo biloba (Ginkgo) (Maidenhair tree)
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 sitei40D-ribose 5-phosphateBy similarity1
Active sitei97Schiff-base intermediate with D-ribose 5-phosphateBy similarity1
Binding sitei169D-ribose 5-phosphate; via amide nitrogenBy similarity1
Binding sitei181Glyceraldehyde 3-phosphateBy similarity1
Binding sitei230D-ribose 5-phosphate; via amide nitrogenBy similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLyase
LigandPyridoxal phosphate, Schiff base

Enzyme and pathway databases

UniPathwayi
UPA00245

Names & Taxonomyi

Protein namesi
Recommended name:
Probable pyridoxal 5'-phosphate synthase subunit PDX1 (EC:4.3.3.6)
Short name:
PLP synthase subunit PDX1
Alternative name(s):
Sor-like protein
Gene namesi
Name:PDX1
OrganismiGinkgo biloba (Ginkgo) (Maidenhair tree)
Taxonomic identifieri3311 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaGinkgoidaeGinkgoalesGinkgoaceaeGinkgo

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001093701 – 309Probable pyridoxal 5'-phosphate synthase subunit PDX1Add BLAST309

Proteomic databases

PRIDEiQ9AT63

Structurei

3D structure databases

ProteinModelPortaliQ9AT63
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni251 – 252D-ribose 5-phosphate bindingBy similarity2

Sequence similaritiesi

Belongs to the PdxS/SNZ family.Curated

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.

Q9AT63-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MASDGVVTVY GDGAITDTKV SSYAVKVGLA QMLRGGVIMD VVNAEQARIA
60 70 80 90 100
EEAGATAVMA LERVPADIRA QGGVARMSDP GLIKEIKSAV TIPVMAKARI
110 120 130 140 150
GHFVEAQILE AIGIDYIDES EVLTPADDXH HINKHNFRIP FVCGCRNLGE
160 170 180 190 200
ALRRIAEGAA MIRTKGEAGT GNVIEAVRHV RSVLGDIRKL QSLDDDEVFA
210 220 230 240 250
FAKQIAAPYE LVRQTKQLGR LPVVNFAAGG VATPADAALM MQLGCDGVFV
260 270 280 290 300
GSGVFKSGDP ARRARAIVQA VTHYNDPHIL AEVSCSLGEA MVGINLKDEK

VERYAERSE
Length:309
Mass (Da):32,945
Last modified:June 1, 2001 - v1
Checksum:iF4E3FD6698D1D235
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF344827 mRNA Translation: AAK18310.1

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF344827 mRNA Translation: AAK18310.1

3D structure databases

ProteinModelPortaliQ9AT63
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiQ9AT63

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayi
UPA00245

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
ProtoNetiSearch...

Entry informationi

Entry nameiPDX1_GINBI
AccessioniPrimary (citable) accession number: Q9AT63
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 15, 2004
Last sequence update: June 1, 2001
Last modified: May 10, 2017
This is version 62 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
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Main funding by: National Institutes of Health

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