Genome location: Pf3D7_14_v3:2,301,208..2,302,942(-)
Genome classification: Core
Product Description: serine hydroxymethyltransferase
SignalP Peptide: N/A
# Transmembrane Domains: 0
EC Numbers: 2.1.2.1 (Glycine hydroxymethyltransferase)
Curated GO (PlasmoDB):
| Type | GO Term | Name |
|---|---|---|
| Component | GO:0005739 | mitochondrion |
| Function | GO:0016597 | amino acid binding |
| Function | GO:0050897 | cobalt ion binding |
| Function | GO:0004372 | glycine hydroxymethyltransferase activity |
| Function | GO:0030170 | pyridoxal phosphate binding |
| Function | GO:0070905 | serine binding |
| Function | GO:0008270 | zinc ion binding |
| Process | GO:0006565 | L-serine catabolic process |
| Process | GO:1904482 | cellular response to tetrahydrofolate |
| Process | GO:0046655 | folic acid metabolic process |
| Process | GO:0019264 | glycine biosynthetic process from serine |
| Process | GO:0006544 | glycine metabolic process |
| Process | GO:0006730 | one-carbon metabolic process |
| Process | GO:0046653 | tetrahydrofolate metabolic process |
Expression by stage (LR - Le Roch et al., and MCA - Malaria Cell Atlas):
| Stage | LR class | MCA mean | MCA prop. zeros |
|---|---|---|---|
| Sporozoite | not expressed | N/A | N/A |
| Ring | not expressed | 0.01 | 0.99 |
| Trophozoite | not expressed | 0.06 | 0.96 |
| Schizont | not expressed | 0.00 | 1.00 |
| Gametocyte | not expressed | 0.05 | 0.97 |
More info:
Old (Pf3D7v3) Gene ID: PF3D7_1456100
Resistome Missense Mutations: None
Resistome Compounds with Missense Mutations: None
Resistome # Samples with Disruptive Mutations: 0 (0 missense, 0 "interesting" missense)
Zhang Phenotype: Mutable in CDS
MIS: 0.916 | MFS: -2.908 | #Insertions: 2
PlasmoGEM Phenotype: Slow (Pb ortholog: PBANKA_1319800)
RMgmDB ABS Phenotype: Different from wild type (Pb ortholog: PBANKA_1319800)
Modification: Disrupted | RMgm-3503
More info: PhenoPlasm Link
AlphaFill Uniprot ID: Q8IKR8
"Best" AlphaFill ligand hit: PLP (pyridoxal-5'-phosphate, Local RMSD=0.07) with 6QVG (Global RMSD=4.26)
BRENDA EC Inhibitors:
| EC # | Name | EC Inhibitors |
|---|---|---|
| 2.1.2.1 | glycine hydroxymethyltransferase | KClSDSKCNDTTNaFGR1NAD+EDTAPCMBCTABNH2OHD1694... |
No evidence of orthology to BindingDB entries
MalariaGEN Pf7 (worldwide samples) # unique SNV/indels:
Homozygous genotype calls only
| variant type | common | rare | doubleton | singleton |
|---|---|---|---|---|
| synonymous | 0 | 18 | 13 | 40 |
| disruptive | 9 | 53 | 41 | 92 |
| missense | 9 | 52 | 39 | 83 |
Any inclusion in genotype call
| variant type | common | rare | doubleton | singleton |
|---|---|---|---|---|
| synonymous | 5 | 41 | 24 | 50 |
| disruptive | 17 | 135 | 83 | 150 |
| missense | 16 | 119 | 67 | 105 |
PlasmoDB Total SNPs: 91
Non-coding: 63 | Synonymous: 17 | Nonsynonymous: 9 | Stop Codon: 2
Protein Length: 462 | Molecular Weight (kDa): 55.24
UniProt ID(s): Q8IKR8
PDB ID(s): None
Isoelectric Point: 8.34
Protein Domain Annotations:
| Source | Family ID | Description |
|---|---|---|
| InterPro | IPR001085 | Serine hydroxymethyltransferase |
| InterPro | IPR015424 | Pyridoxal phosphate-dependent transferase |
| InterPro | IPR039429 | Serine hydroxymethyltransferase-like domain |
| PFam | PF00464 | Serine hydroxymethyltransferase-like domain |
| Superfamily | SSF53383 | Pyridoxal phosphate-dependent transferase |
| PMID | Title | Authors | DOI/Link |
|---|---|---|---|
| 12368864 | Genome sequence of the human malaria parasite Plasmodium falciparum. | Gardner MJ, Hall N, ..., Barrell B | 10.1038/nature01097 |
| 19591883 | Catalytic and ligand-binding characteristics of Plasmodium falciparum serinehydroxymethyltransferase. | Pang CK, Hunter JH, ..., Rathod PK | 10.1016/j.molbiopara.2009.06.011 |
| 21129192 | Dynamic subcellular localization of isoforms of the folate pathway enzyme serinehydroxymethyltransferase (SHMT) through the erythrocytic cycle of Plasmodiumfalciparum. | Read M, Muller IB, ..., Hyde JE | 10.1186/1475-2875-9-351 |
| 33821563 | Non-canonical metabolic pathways in the malaria parasite detected byisotope-tracing metabolomics. | Cobbold SA, V Tutor M, ..., McConville MJ | 10.15252/msb.202010023 |
| 37810721 | In Silico and In Vitro Potential of FDA-Approved Drugs for Antimalarial DrugRepurposing against Plasmodium Serine Hydroxymethyltransferases | Mee-Udorn P, Phiwkaow K, ..., Rungrotmongkol T | 10.1021/acsomega.3c01309 |
| 37543353 | Mangiferin is a new potential antimalarial and anticancer drug for targetingserine hydroxymethyltransferase | Maenpuen S, Mee-Udorn P, ..., Chitnumsub P | 10.1016/j.abb.2023.109712 |