Detailed view for MUL_0823

Basic information

TDR Targets ID: 951598
Mycobacterium ulcerans, D-3-phosphoglycerate dehydrogenase
Source Database / ID:  KEGG  

pI: 6.0279 | Length (AA): 329 | MW (Da): 34782 | 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

PF00389   D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
PF02826   D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0016616   oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor  
GO:0051287   NAD binding  
GO:0055114   oxidation reduction  
GO:0008152   metabolic process  

Structural information

Modbase 3D models:

There are 4 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
2 328 1sc6 (A) 8 331 29.00 0 1 1.18582 0.1
4 327 6bii (A) 2 326 38.00 0 1 1.3922 -0.36
150 186 1bvu (A) 203 240 27.00 0.44 0.11 0.221562 1.42
152 186 3aoe (E) 212 246 40.00 0.56 0.22 0.418483 1

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_126787)

Species Accession Gene Product
Arabidopsis thaliana AT1G68010   hydroxypyruvate reductase
Arabidopsis thaliana AT1G79870   glyoxylate/hydroxypyruvate reductase A HPR2
Candida albicans CaO19.11068   one of 4 genes similar to S. cerevisiae YNL274C, a putative hydroxyisocaproate dehydrogenase
Candida albicans CaO19.2989   one of 4 genes similar to S. cerevisiae YNL274C, a putative hydroxyisocaproate dehydrogenase
Candida albicans CaO19.10506   one of 4 genes similar to S. cerevisiae YNL274C, a putative hydroxyisocaproate dehydrogenase
Candida albicans CaO19.225   one of 4 genes similar to S. cerevisiae YNL274C, a putative hydroxyisocaproate dehydrogenase
Candida albicans CaO19.3584   one of 4 genes similar to S. cerevisiae YNL274C, a putative hydroxyisocaproate dehydrogenase
Candida albicans CaO19.2176   one of 4 genes similar to S. cerevisiae YNL274C, a putative hydroxyisocaproate dehydrogenase
Candida albicans CaO19.9722   one of 4 genes similar to S. cerevisiae YNL274C, a putative hydroxyisocaproate dehydrogenase
Candida albicans CaO19.7855   one of 4 genes similar to S. cerevisiae YNL274C, a putative hydroxyisocaproate dehydrogenase
Dictyostelium discoideum DDB_G0292104   2-keto-D-gluconate reductase
Drosophila melanogaster Dmel_CG1236   CG1236 gene product from transcript CG1236-RA
Drosophila melanogaster Dmel_CG9331   CG9331 gene product from transcript CG9331-RK
Drosophila melanogaster Dmel_CG31674   CG31674 gene product from transcript CG31674-RA
Drosophila melanogaster Dmel_CG31673   CG31673 gene product from transcript CG31673-RB
Escherichia coli b3553   glyoxylate/hydroxypyruvate reductase B
Echinococcus granulosus EgrG_000332000   glyoxylate reductase:hydroxypyruvate reductase
Entamoeba histolytica EHI_134030   D-glycerate dehydrogenase, putative
Echinococcus multilocularis EmuJ_000332000   glyoxylate reductase:hydroxypyruvate reductase
Homo sapiens ENSG00000137106   glyoxylate reductase/hydroxypyruvate reductase
Mus musculus ENSMUSG00000035637   glyoxylate reductase/hydroxypyruvate reductase
Mycobacterium tuberculosis Rv0728c   Possible D-3-phosphoglycerate dehydrogenase SerA2 (phosphoglycerate dehydrogenase) (PGDH)
Mycobacterium ulcerans MUL_0823   D-3-phosphoglycerate dehydrogenase
Oryza sativa 4334916   Os04g0107500
Oryza sativa 4327981   Os02g0101500
Oryza sativa 4334913   Os04g0106400
Oryza sativa 4334914   Os04g0107200
Oryza sativa 4327189   Os01g0228600
Oryza sativa 9269852   Os07g0597625
Oryza sativa 4334915   Os04g0107300
Saccharomyces cerevisiae YNL274C   Gor1p
Schmidtea mediterranea mk4.029167.02  
Schmidtea mediterranea mk4.080464.00   Glyoxylate reductase/hydroxypyruvate reductase
Schmidtea mediterranea mk4.037089.02  
Schmidtea mediterranea mk4.001537.02  
Schmidtea mediterranea mk4.003144.00  
Trichomonas vaginalis TVAG_119160   2-hydroxyacid dehydrogenase, putative
Trichomonas vaginalis TVAG_047210   2-hydroxyacid dehydrogenase, putative

Essentiality

MUL_0823 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
b3553 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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
  • 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
  • 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

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
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

No literature references available for this target.

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

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Gene identifier MUL_0823 (Mycobacterium ulcerans), D-3-phosphoglycerate dehydrogenase
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