Detailed view for Tb927.4.360

Basic information

TDR Targets ID: 12112
Trypanosoma brucei, 1,2-Dihydroxy-3-keto-5-methylthiopentene dioxygenase, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.7611 | Length (AA): 280 | MW (Da): 33471 | Paralog Number: 0

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

Druggability Group : DG1

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

PF03079   ARD/ARD' family

Gene Ontology

Mouse over links to read term descriptions.
GO:0010309   acireductone dioxygenase [iron(II)-requiring] activity  
GO:0051213   dioxygenase activity  
GO:0046872   metal ion binding  
GO:0055114   oxidation reduction  
GO:0019509   methionine salvage  

Metabolic Pathways

Cysteine and methionine metabolism (KEGG)
Global map (KEGG)

Structural information

Modbase 3D models:

There are 6 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 45 2a9u (A) 95 139 24.00 0.65 0.11 0.742714 -3.54
3 57 2lw9 (A) 1 51 39.00 0.42 0.07 0.673429 -1.73
7 66 5hmo (A) 813 863 53.00 0.00026 0.02 0.814086 -2.46
12 55 5f5s (B) 273 318 41.00 0.49 0.07 0.858143 -3.47
90 270 4qgn (A) 1 177 31.00 0 1 1.01943 -0.66
90 269 5i8t (A) 1 176 36.00 0 1 1.03266 -0.68

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 80-100% percentile Procyclic, Bloodstream Form. Siegel TN
Show/Hide expression data references
  • Siegel TN Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites.

Orthologs

Ortholog group members (OG5_128685)

Species Accession Gene Product
Arabidopsis thaliana AT5G43850   acireductone dioxygenase 4
Arabidopsis thaliana AT4G14716   acireductone dioxygenase 1
Arabidopsis thaliana AT2G26400   acireductone dioxygenase 3
Arabidopsis thaliana AT4G14710   acireductone dioxygenase 2
Candida albicans CaO19.9842   similar to MMSAB operon regulatory protein
Candida albicans CaO19.2306   similar to MMSAB operon regulatory protein
Caenorhabditis elegans CELE_F42F12.4   Protein F42F12.4
Dictyostelium discoideum DDB_G0291376   ARD/ARD' family protein
Drosophila melanogaster Dmel_CG32068   CG32068 gene product from transcript CG32068-RB
Homo sapiens ENSG00000182551   acireductone dioxygenase 1
Leishmania braziliensis LbrM.20.4060   1,2-Dihydroxy-3-keto-5-methylthiopentene dioxygenase, putative;with=GeneDB:LmjF34.4600
Leishmania donovani LdBPK_344230.1   1,2-Dihydroxy-3-keto-5-methylthiopentene dioxygenase, putative
Leishmania infantum LinJ.34.4230   1,2-Dihydroxy-3-keto-5-methylthiopentene dioxygenase, putative;with=GeneDB:LmjF34.4600
Leishmania major LmjF.34.4600   1,2-Dihydroxy-3-keto-5-methylthiopentene dioxygenase, putative
Leishmania mexicana LmxM.33.4600   hypothetical protein, conserved
Mus musculus ENSMUSG00000020629   acireductone dioxygenase 1
Oryza sativa 4348646   Os10g0419400
Oryza sativa 4331707   Os03g0161800
Oryza sativa 4348647   Os10g0419500
Saccharomyces cerevisiae YMR009W   acireductone dioxygenase (Ni2+-requiring)
Schmidtea mediterranea mk4.046052.01  
Schmidtea mediterranea mk4.000784.05   1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase
Trypanosoma brucei gambiense Tbg972.4.60   hypothetical protein, conserved
Trypanosoma brucei Tb927.4.360   1,2-Dihydroxy-3-keto-5-methylthiopentene dioxygenase, putative
Trypanosoma congolense TcIL3000_4_20   1,2-Dihydroxy-3-keto-5-methylthiopentene dioxygenase, putative
Trypanosoma cruzi TcCLB.507873.60   1,2-Dihydroxy-3-keto-5-methylthiopentene dioxygenase, putative
Trypanosoma cruzi TcCLB.510691.10   1,2-Dihydroxy-3-keto-5-methylthiopentene dioxygenase, putative

Essentiality

Tb927.4.360 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
Tb927.4.360 this record Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.4.360 this record Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.4.360 this record Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.4.360 this record Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
Show/Hide essentiality data references
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
cell proliferation (GO:0008283) increased (PATO:0000470) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: increased cell proliferation (significant gain of fitness) in bloodstream forms (stage 3 days). References: 21363968
cell proliferation (GO:0008283) normal (PATO:0000461) bloodstream stage trypomastigotes (PLO:0027) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain of fitness) in bloodstream forms (stage 6 days). References: 21363968
cell proliferation (GO:0008283) normal (PATO:0000461) procyclic (PLO:0034) inferred from RNAi experiment (ECO:0000019) No drug identifiers listed for this gene.
Annotator: fernan@iib.unsam.edu.ar. Comment: normal cell proliferation (no significant loss or gain of fitness) in differentiation of procyclic to bloodstream forms . References: 21363968

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
Non orthologous druggable targets
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

No reagent availability information for this target.

Bibliographic References

1 literature reference was collected for this gene.

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Gene identifier Tb927.4.360 (Trypanosoma brucei), 1,2-Dihydroxy-3-keto-5-methylthiopentene dioxygenase, putative
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