PF3D7_0621200 (PDX1)

Genome location: Pf3D7_06_v3:871,089..873,059(-)

Genome classification: Core

Function and Localization

Product Description: pyridoxine biosynthesis protein PDX1

SignalP Peptide: N/A

# Transmembrane Domains: 0

EC Numbers: 4.3.3.6 (Pyridoxal 5'-phosphate synthase (glutamine hydrolyzing))

Curated GO (PlasmoDB):

Type	GO Term	Name
Component	GO:0005829	cytosol
Component	GO:1903561	extracellular vesicle
Component	GO:0005634	nucleus
Function	GO:0016843	amine-lyase activity
Function	GO:0003824	catalytic activity
Function	GO:0004359	glutaminase activity
Function	GO:0042802	identical protein binding
Process	GO:0006520	cellular amino acid metabolic process
Process	GO:0042823	pyridoxal phosphate biosynthetic process
Process	GO:0008615	pyridoxine biosynthetic process
Process	GO:0000304	response to singlet oxygen
Process	GO:0042819	vitamin B6 biosynthetic process

Expression by stage (LR - Le Roch et al., and MCA - Malaria Cell Atlas):

Stage	LR class	MCA mean	MCA prop. zeros
Sporozoite	possibly expressed	N/A	N/A
Ring	expressed	0.64	0.72
Trophozoite	expressed	1.06	0.55
Schizont	expressed	0.10	0.95
Gametocyte	expressed	0.59	0.68

More info:

Resistome Mutations

Old (Pf3D7v3) Gene ID: PF3D7_0621200

Resistome Missense Mutations: None

Resistome Compounds with Missense Mutations: None

Resistome # Samples with Disruptive Mutations: 0 (0 missense, 0 "interesting" missense)

Essentiality (ABS)

Zhang Phenotype: Mutable in CDS

MIS: 0.919 | MFS: -2.67 | #Insertions: 1

PlasmoGEM Phenotype: Dispensable (Pb ortholog: PBANKA_1120200)

Relative Growth Rate: 0.91 ± 0.17
Confidence: 4.98

RMgmDB ABS Phenotype: Different from wild type (Pb ortholog: PBANKA_1120200)

Modification: Disrupted | RMgm-3035

More info: PhenoPlasm Link

Binding Evidence

AlphaFill Uniprot ID: C6KT50

"Best" AlphaFill ligand hit: PLP (pyridoxal-5'-phosphate, Local RMSD=0.04) with 5LNR (Global RMSD=0.99)

BRENDA EC Inhibitors:

EC #	Name	EC Inhibitors
4.3.3.6	pyridoxal 5'-phosphate synthase (glutamine hydrolysing)	acivicinD-erythroseD-erythronhydrazideD-erythrose 4-phosphate2-deoxy-D-ribose 5-phosphate4-phospho-D-erythronhydrazide

No evidence of orthology to BindingDB entries

Orthology Information

Ortholog Group (OrthoMCL): OG6_102840

No human ortholog(s)

Genetic Variation

MalariaGEN Pf7 (worldwide samples) # unique SNV/indels:

Homozygous genotype calls only

variant type	common	rare	doubleton	singleton
synonymous	1	13	7	20
disruptive	0	9	7	13
missense	0	9	7	11

Any inclusion in genotype call

variant type	common	rare	doubleton	singleton
synonymous	2	25	16	20
disruptive	4	23	15	50
missense	3	20	13	39

PlasmoDB Total SNPs: 101

Non-coding: 94 | Synonymous: 5 | Nonsynonymous: 2 | Stop Codon: 0

Protein Information

Protein Length: 301 | Molecular Weight (kDa): 33.013

UniProt ID(s): C6KT50

PDB ID(s): None

Isoelectric Point: 7.16

Protein Domain Annotations:

Source	Family ID	Description
InterPro	IPR001852	Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ
InterPro	IPR011060	Ribulose-phosphate binding barrel
InterPro	IPR033755	PdxS/SNZ N-terminal domain
PFam	PF01680	PdxS/SNZ N-terminal domain
Superfamily	SSF51366	Ribulose-phosphate binding barrel

PMID	Title	Authors	DOI/Link
12368867	Sequence of Plasmodium falciparum chromosomes 1, 3-9 and 13.	Hall N, Pain A, ..., Barrell BG	10.1038/nature01095
15590634	Analysis of the vitamin B6 biosynthesis pathway in the human malaria parasitePlasmodium falciparum.	Wrenger C, Eschbach ML, ..., Walter RD	10.1074/jbc.M412475200
23181666	Organellar proteomics reveals hundreds of novel nuclear proteins in the malariaparasite Plasmodium falciparum.	Oehring SC, Woodcroft BJ, ..., Voss TS	10.1186/gb-2012-13-11-r108
28944300	Proteomic analysis of extracellular vesicles from a Plasmodium falciparum Kenyanclinical isolate defines a core parasite secretome.	Abdi A, Yu L, ..., Rayner J	10.12688/wellcomeopenres.11910.2
30379851	Identification of Plasmodium falciparum nuclear proteins by mass spectrometry andproposed protein annotation.	Briquet S, Ourimi A, ..., Vaquero C	10.1371/journal.pone.0205596