Detailed view for LmjF.06.0730

Basic information

TDR Targets ID: 25073
Leishmania major, serine-threonine dehydratase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 8.1732 | Length (AA): 338 | MW (Da): 37046 | Paralog Number: 0

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

Druggability Group : DG2

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

PF00291   Pyridoxal-phosphate dependent enzyme

Gene Ontology

Mouse over links to read term descriptions.
GO:0030170   pyridoxal phosphate binding  
GO:0003824   catalytic activity  
GO:0008152   metabolic process  

Structural information

Modbase 3D models:

There are 5 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
1 338 1vb3 (A) 46 394 14.00 0 1 1.15 0.16
2 328 1ve5 (A) 2 310 35.00 0 1 1.42 -1.01
1 336 1v71 (A) 7 323 26.00 0.00000000031 1 1.31398 -0.33
2 328 1ve5 (A) 2 310 35.00 0 1 1.35346 -0.37
2 336 3l6b (A) 7 329 35.00 0.00000014 1 1.41102 -0.63

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:

No structure availble in the PDB for this protein

Expression

Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile metacyclic. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile amastigotes. Fernandes MC
Show/Hide expression data references
  • Fernandes MC Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures.

Orthologs

Ortholog group members (OG5_126759)

Species Accession Gene Product
Arabidopsis thaliana AT4G11640   serine racemase
Arabidopsis thaliana AT3G10050   threonine dehydratase
Brugia malayi Bm1_24445   Pyridoxal-phosphate dependent enzyme family protein
Candida albicans CaO19.12935   serine and threonine dehydratase
Candida albicans CaO19.5480   serine and threonine dehydratase
Caenorhabditis elegans CELE_T01H8.2   Protein T01H8.2
Caenorhabditis elegans CELE_Y51H7C.9   Protein Y51H7C.9
Caenorhabditis elegans CELE_K01C8.1   Protein K01C8.1
Dictyostelium discoideum DDB_G0289463   serine racemase
Dictyostelium discoideum DDB_G0277245   serine/threonine dehydratase
Drosophila melanogaster Dmel_CG8129   CG8129 gene product from transcript CG8129-RB
Escherichia coli b3772   L-threonine dehydratase, biosynthetic
Escherichia coli b3117   L-threonine dehydratase, catabolic
Entamoeba histolytica EHI_092390   threonine dehydratase, putative
Entamoeba histolytica EHI_049910   threonine dehydratase, putative
Entamoeba histolytica EHI_126080   threonine dehydratase, putative
Giardia lamblia GL50803_12108   Threonine dehydratase lateral transfer candidate
Homo sapiens ENSG00000167720   serine racemase
Leishmania braziliensis LbrM.06.0720   serine-threonine dehydratase, putative;with=GeneDB:LmjF06.0730
Leishmania donovani LdBPK_060760.1   threonine ammonia-lyase
Leishmania infantum LinJ.06.0760   serine-threonine dehydratase, putative;with=GeneDB:LmjF06.0730
Leishmania major LmjF.06.0730   serine-threonine dehydratase, putative
Leishmania mexicana LmxM.06.0730   threonine ammonia-lyase
Loa Loa (eye worm) LOAG_01358   hypothetical protein
Mycobacterium leprae ML1209   Probable threonine dehydratase IlvA
Mus musculus ENSMUSG00000001323   serine racemase
Mycobacterium tuberculosis Rv1559   Probable threonine dehydratase IlvA
Mycobacterium ulcerans MUL_1550   threonine dehydratase
Oryza sativa 4333898   Os03g0713000
Oryza sativa 4336624   Os04g0555900
Onchocerca volvulus OVOC248   Serine racemase homolog
Saccharomyces cerevisiae YKL218C   threo-3-hydroxy-L-aspartate ammonia-lyase SRY1
Saccharomyces cerevisiae YER086W   threonine ammonia-lyase ILV1
Schistosoma japonicum Sjp_0009260   ko:K01754 threonine dehydratase [EC4.3.1.19], putative
Schistosoma mansoni Smp_137520   threonine dehydratase/deaminase
Schmidtea mediterranea mk4.000335.03  
Schmidtea mediterranea mk4.003368.00  
Schmidtea mediterranea mk4.008838.02   Threonine dehydratase/deaminase, putative
Schmidtea mediterranea mk4.020045.00   Threonine dehydratase/deaminase, putative
Trypanosoma cruzi TcCLB.506681.70   serine-threonine dehydratase, putative
Trypanosoma cruzi TcCLB.506825.70   serine-threonine dehydratase, putative
Trichomonas vaginalis TVAG_362020   threonine dehydratase/deaminase, putative
Trichomonas vaginalis TVAG_090490   threonine dehydratase/deaminase, putative
Trichomonas vaginalis TVAG_375350   threonine dehydratase/deaminase, putative

Essentiality

LmjF.06.0730 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b3117 Escherichia coli non-essential goodall
b3772 Escherichia coli non-essential goodall
CELE_Y51H7C.9 Caenorhabditis elegans slow growth wormbase
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

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
Mus musculus serine racemase Compounds References
Homo sapiens serine racemase Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

No enough druggable targets predicted through repurposing network model to make a plot

Putative Drugs List

Compound Raw Global Species
0.0036 0.5334 0.5

Assayability

Assay information

No assay information for this target.

Reagent availability

  • Lmaj009745AAA;
  • Type Source Notes
    soluble recombinant protein Structural Genomics for Pathogenic Protozoa (SGPP) Lmaj009745; Recombinant protein: full-length; Source: L major; threonine dehydratase-like protein ;

Bibliographic References

1 literature reference was collected for this gene.

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

User comments

No user comments are available for this gene. Log in to add comments, or register.

Enter your comment

User ()
Gene identifier LmjF.06.0730 (Leishmania major), serine-threonine dehydratase, putative
Title for this comment
Comment