Detailed view for PF3D7_1235600

Basic information

TDR Targets ID: 5397
Plasmodium falciparum, serine hydroxymethyltransferase
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 8.0599 | Length (AA): 442 | MW (Da): 49780 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG3

Targets have been classified into druggability groups (DG) according to their druggability score in network driven prioritizations. DGs range from 1 to 5; the higher the group number, the higher the chance of the target to be druggable

Pfam domains

PF00464   Serine hydroxymethyltransferase

Gene Ontology

Mouse over links to read term descriptions.
GO:0035999   GO:tetrahydrofolate interconversion  

GO:0019264   glycine biosynthetic process from serine  
GO:0005575   cellular_component  
GO:0030170   pyridoxal phosphate binding  
GO:0004372   glycine hydroxymethyltransferase activity  
GO:0003824   catalytic activity  
GO:0006730   one-carbon compound metabolic process  
GO:0006563   L-serine metabolic process  
GO:0006544   glycine metabolic process  

Structural information

Modbase 3D models:

There are 3 models calculated for this protein. More info on these models, including the models themselves is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
1 441 1dfo (A) 2 415 40.00 0 1 1.45 -0.96
4 441 1rv3 (A) 23 478 47.00 0 1 1.63 -1.69
1 442 4o6z (A) 1 442 99.99 0 1 2.2309 -1.42

Help me make sense of these data.

Target Beg: first modeled residue
Target End: last modeled residue
Template: template structure used for modelling (PDB accession and chain)
Template Beg: first template residue in target-template alignment
Template End: last template residue in target-template alignment
Identity: sequence identity
Evalue: E value for target-template hit
Model Score: GA341 score (>0.7 for reliable model)
MPQS: ModPipe Quality Score (>1.1 for reliable model)
zDope: zDope Score (negative for reliable model)

A more detailed description of these scores is available at the Modbase Model Evaluation Help Pages, and in the papers referenced therein.

PDB Structures:

PDB tag
  • 4O6Z:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, Oocyst, Female Gametocyte, Male Gametocyte. Otto TD Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, early schizont, late trophozoite, Ring. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile early trophozoite, late schizont. PlasmoDB
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile Sporozoite. Zanghi G
Show/Hide expression data references
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.

Orthologs

Ortholog group members (OG5_126679)

Species Accession Gene Product
Arabidopsis thaliana AT5G26780   serine hydroxymethyltransferase 2
Arabidopsis thaliana AT4G32520   serine hydroxymethyltransferase 3
Arabidopsis thaliana AT4G37930   serine transhydroxymethyltransferase 1
Arabidopsis thaliana AT4G13890   serine hydroxymethyltransferase 5
Arabidopsis thaliana AT4G13930   serine hydroxymethyltransferase 4
Babesia bovis BBOV_IV005840   serine hydroxymethyltransferase, putative
Brugia malayi Bm1_45050   Serine hydroxymethyltransferase
Candida albicans CaO19.13173   serine hydroxymethyl transferase II, similar to S. cerevisiae SHM2 (YLR058C)
Candida albicans CaO19.1342   serine hydroxymethyl transferase I, similar to S. cerevisiae SHM1 (YBR263W)
Candida albicans CaO19.8922   serine hydroxymethyl transferase I, similar to S. cerevisiae SHM1 (YBR263W)
Candida albicans CaO19_1342   hypothetical protein
Candida albicans CaO19.5750   serine hydroxymethyl transferase II, similar to S. cerevisiae SHM2 (YLR058C)
Caenorhabditis elegans CELE_C05D11.11   Protein MEL-32, isoform A
Cryptosporidium hominis Chro.80306   serine hydroxymethyltransferase
Cryptosporidium parvum cgd8_2610   cytosolic serine hydroxymethyl transferase
Chlamydia trachomatis CT_432   serine hydroxymethyltransferase
Dictyostelium discoideum DDB_G0291652   serine hydroxymethyltransferase
Dictyostelium discoideum DDB_G0277947   serine hydroxymethyltransferase
Drosophila melanogaster Dmel_CG3011   CG3011 gene product from transcript CG3011-RA
Escherichia coli b2551   serine hydroxymethyltransferase
Echinococcus granulosus EgrG_000376600   Maternal Effect Lethal family member mel 32
Echinococcus multilocularis EmuJ_000376600   Maternal Effect Lethal family member (mel 32)
Homo sapiens ENSG00000176974   serine hydroxymethyltransferase 1 (soluble)
Homo sapiens ENSG00000182199   serine hydroxymethyltransferase 2 (mitochondrial)
Leishmania braziliensis LbrM.14.1490   serine hydroxymethyltranferase (SHMT-S)
Leishmania braziliensis LbrM.28.2560   serine hydroxymethyltransferase (SHMT-L)
Leishmania donovani LdBPK_282530.1   serine hydroxymethyltransferase (SHMT-L)
Leishmania donovani LdBPK_141400.1   serine hydroxymethyltranferase (SHMT-S)
Leishmania infantum LinJ.14.1400   serine hydroxymethyltranferase (SHMT-S)
Leishmania infantum LinJ.28.2530   serine hydroxymethyltransferase (SHMT-L)
Leishmania major LmjF.14.1320   serine hydroxymethyltranferase (SHMT-S)
Leishmania major LmjF.28.2370   serine hydroxymethyltransferase (SHMT-L)
Leishmania mexicana LmxM.14.1320   serine hydroxymethyltransferase, putative
Leishmania mexicana LmxM.28.2370   serine hydroxymethyltransferase
Loa Loa (eye worm) LOAG_01448   hypothetical protein
Mycobacterium leprae ML1953c   Probable Serine hydroxymethyltransferase 1 GlyA
Mus musculus ENSMUSG00000025403   serine hydroxymethyltransferase 2 (mitochondrial)
Mus musculus ENSMUSG00000020534   serine hydroxymethyltransferase 1 (soluble)
Mycobacterium tuberculosis Rv1093   Serine hydroxymethyltransferase 1 GlyA1
Mycobacterium tuberculosis Rv0070c   Serine hydroxymethyltransferase GlyA2 (serine methylase 2) (SHMT 2)
Mycobacterium ulcerans MUL_4902   serine hydroxymethyltransferase
Mycobacterium ulcerans MUL_0188   serine hydroxymethyltransferase
Neospora caninum NCLIV_049400   Serine hydroxymethyltransferase (EC 2.1.2.1), related
Oryza sativa 4334048   Os03g0738400
Oryza sativa 4352058   Os12g0409000
Oryza sativa 4350456   Os11g0455800
Onchocerca volvulus OVOC7396  
Plasmodium berghei PBANKA_1450200   serine hydroxymethyltransferase, putative
Plasmodium falciparum PF3D7_1235600   serine hydroxymethyltransferase
Plasmodium knowlesi PKNH_1455300   serine hydroxymethyltransferase, putative
Plasmodium vivax PVX_100730   serine hydroxymethyltransferase, putative
Plasmodium yoelii PY00962   Serine hydroxymethyltransferase
Saccharomyces cerevisiae YLR058C   glycine hydroxymethyltransferase SHM2
Saccharomyces cerevisiae YBR263W   glycine hydroxymethyltransferase SHM1
Schistosoma japonicum Sjp_0019350   Serine hydroxymethyltransferase, mitochondrial precursor, putative
Schistosoma japonicum Sjp_0200420   ko:K00600 glycine hydroxymethyltransferase [EC2.1.2.1], putative
Schistosoma japonicum Sjp_0019340   Serine hydroxymethyltransferase, mitochondrial precursor, putative
Schistosoma mansoni Smp_179710   serine hydroxymethyltransferase
Schistosoma mansoni Smp_144570   serine hydroxymethyltransferase
Schmidtea mediterranea mk4.005875.01   Serine hydroxymethyltransferase, cytosolic
Schmidtea mediterranea mk4.006071.02   Serine hydroxymethyltransferase, cytosolic
Schmidtea mediterranea mk4.000652.02   Serine hydroxymethyltransferase, cytosolic
Schmidtea mediterranea mk4.006071.01   Serine hydroxymethyltransferase
Trypanosoma cruzi TcCLB.509937.150   serine hydroxymethyltransferase, putative
Trypanosoma cruzi TcCLB.510407.90   serine hydroxymethyltransferase, putative
Toxoplasma gondii TGME49_234190   serine hydroxymethyltransferase 2, putative
Treponema pallidum TP0329   serine hydroxymethyltransferase
Theileria parva TP01_0390   serine hydroxymethyltransferase, putative
Trichomonas vaginalis TVAG_109540   serine hydroxymethyltransferase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0005   serine hydroxymethyltransferase

Essentiality

PF3D7_1235600 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu70 Mycobacterium tuberculosis non-essential nmpdr
b2551 Escherichia coli essential goodall
CELE_C05D11.11 Caenorhabditis elegans embryonic lethal wormbase
TGME49_234190 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • sidik A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. Sidik, Saima M., et al. "A genome-wide CRISPR screen in toxoplasma identifies essential apicomplexan genes." Cell 166.6 (2016): 1423-1435.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • plasmo Functional Profiling of a Plasmodium Genome Reveals an Abundance of Essential Genes. Bushell, Ellen, et al. "Functional profiling of a Plasmodium genome reveals an abundance of essential genes." Cell 170.2 (2017): 260-272.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • goodall The Essential Genome of Escherichia coli K-12 (Transposon directed high-throughput mutagenesis) Goodall, Emily CA, et al. "The essential genome of Escherichia coli K-12." mBio 9.1 (2018): e02096-17.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

Phenotypes and Validation (curated)

We have no manually annotated phenotypes for this target. What does this mean? / Care to help?

In TDR Targets, information about phenotypes that are caused by drugs, or by genetic manipulation of cells (e.g. gene knockouts or knockdowns) is manually curated from the literature. These descriptions help to describe the potential of the target for drug development. If no information is available for this gene or if the information is incomplete, this may mean that i) the papers containing this information either appeared after the curation effort for this organism was carried out or they were inadvertently missed by curators; or that ii) the curation effort for this organism has not yet started.

In any case, if you have information about papers containing relevant validation data for this target, please contact us.

Annotated validation

No validation data for this target

Associated compounds / Druggability

Known modulators for this target

No chemical compounds associated to this gene

Predicted associations

By orthology with druggable targets
Species Known druggable target Linked compounds Reference
Homo sapiens serine hydroxymethyltransferase 1 (soluble) Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

No assay information for this target.

Reagent availability

  • Pfal009319AAA;
  • Type Source Notes
    soluble recombinant protein Structural Genomics for Pathogenic Protozoa (SGPP) Pfal009319; Recombinant protein: full-length; Source: P falciparum; Serine hydroxymethyltransferase ;

Bibliographic References

9 literature references were collected for this gene.

If you have references for this gene, please enter them in a user comment (below) or Contact us.

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Gene identifier PF3D7_1235600 (Plasmodium falciparum), serine hydroxymethyltransferase
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