Detailed view for Rv0858c

Basic information

TDR Targets ID: 7614
Mycobacterium tuberculosis, Probable N-succinyldiaminopimelate aminotransferase DapC (DAP-at)
Source Database / ID:  Tuberculist 

pI: 5.2394 | Length (AA): 397 | MW (Da): 42209 | Paralog Number: 1

Signal peptide: Y | GPI Anchor: | 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

PF00155   Aminotransferase class I and II

Gene Ontology

Mouse over links to read term descriptions.
GO:0030170   pyridoxal phosphate binding  
GO:0016847   1-aminocyclopropane-1-carboxylate synthase activity  
GO:0003824   catalytic activity  
GO:0009058   biosynthetic process  

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
2 393 2o0r (A) 2 393 99.99 0 1 2.19471 -1.35

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
  • 2O0R:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Dormant phase. hasan
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile Dormant phase. murphy
Show/Hide expression data references
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.

Orthologs

Ortholog group members (OG5_126697)

Species Accession Gene Product
Arabidopsis thaliana AT2G22250   aspartate aminotransferase
Arabidopsis thaliana AT1G77670   putative aminotransferase
Brugia malayi Bm1_10490   kynurenine-oxoglutarate transaminase
Candida albicans CaO19.5809   similar to S. cerevisiae YJL060W
Candida albicans CaO19.13231   similar to S. cerevisiae YJL060W
Caenorhabditis elegans CELE_R03A10.4   Protein NKAT-3, isoform B
Caenorhabditis elegans CELE_F28H6.3   Protein NKAT-1
Dictyostelium discoideum DDB_G0287269   cysteine-S-conjugate beta-lyase
Drosophila melanogaster Dmel_CG6950   CG6950 gene product from transcript CG6950-RC
Escherichia coli b0600   methionine aminotransferase, PLP-dependent
Entamoeba histolytica EHI_006080   aspartate aminotransferase, putative
Homo sapiens ENSG00000137944   cysteine conjugate-beta lyase 2
Homo sapiens ENSG00000171097   cysteine conjugate-beta lyase, cytoplasmic
Leishmania braziliensis LbrM.33.1600   cysteine conjugate beta-lyase, aminotransferase- like protein
Leishmania donovani LdBPK_331410.1   glutamine aminotransferase, putative
Leishmania infantum LinJ.33.1410   cysteine conjugate beta-lyase, aminotransferase- like protein
Leishmania major LmjF.33.1330   cysteine conjugate beta-lyase, aminotransferase- like protein
Leishmania mexicana LmxM.32.1330   cysteine conjugate beta-lyase, aminotransferase- like protein
Loa Loa (eye worm) LOAG_06544   kynurenine-oxoglutarate transaminase
Mus musculus ENSMUSG00000040213   cysteine conjugate-beta lyase 2
Mus musculus ENSMUSG00000039648   cysteine conjugate-beta lyase 1
Mycobacterium tuberculosis Rv3565   Possible aspartate aminotransferase AspB (transaminase A) (ASPAT) (glutamic--oxaloacetic transaminase) (glutamic--aspartic trans
Mycobacterium tuberculosis Rv0858c   Probable N-succinyldiaminopimelate aminotransferase DapC (DAP-at)
Mycobacterium ulcerans MUL_0297   aminotransferase
Mycobacterium ulcerans MUL_4130   aspartate aminotransferase
Oryza sativa 4324941   Os01g0871300
Oryza sativa 4347242   Os09g0453800
Saccharomyces cerevisiae YJL060W   Bna3p
Schistosoma japonicum Sjp_0317620   Kynurenine--oxoglutarate transaminase 1, putative
Schistosoma japonicum Sjp_0057150   ko:K00816 kynurenine-oxoglutarate transaminase [EC2.6.1.7], putative
Schistosoma japonicum Sjp_0057160   similar to U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1, putative
Schistosoma mansoni Smp_123750   arylformamidase
Schmidtea mediterranea mk4.034199.03  
Schmidtea mediterranea mk4.043355.02  
Schmidtea mediterranea mk4.050221.01  
Schmidtea mediterranea mk4.000043.02   KynurenineALQ-oxoglutarate transaminase 1
Trypanosoma brucei gambiense Tbg972.10.14420   kynurenine aminotransferase, putative
Trypanosoma brucei Tb927.10.11970   glutamine aminotransferase (GlnAT)
Trypanosoma congolense TcIL3000_10_10170   glutamine aminotransferase, putative
Treponema pallidum TP0223   hypothetical protein
Trichomonas vaginalis TVAG_430210   aspartate aminotransferase, putative
Trichomonas vaginalis TVAG_419720   aspartate aminotransferase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0002   aspartate aminotransferase

Essentiality

Rv0858c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu874 this record Mycobacterium tuberculosis non-essential nmpdr
Tb927.10.11970 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.11970 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.11970 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.10.11970 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
b0600 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • 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
  • 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
  • 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.
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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
  • 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)

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

Druggability index (range: 0 to 1): 0.2

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 cysteine conjugate-beta lyase, cytoplasmic Compounds References
Homo sapiens cysteine conjugate-beta lyase 2 Compounds References
By sequence similarity to non orthologous druggable targets
No additional associated druggable targets
Obtained from network model

Ranking Plot

Putative Drugs List

Compound Raw Global Species
0.0106 0.5116 1
0.0213 0.3573 1
0.0125 0.261 1

Assayability

Assay information

No assay information for this target.

Reagent availability

No reagent availability information for this target.

Bibliographic References

152 literature references were collected for this gene.

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Gene identifier Rv0858c (Mycobacterium tuberculosis), Probable N-succinyldiaminopimelate aminotransferase DapC (DAP-at)
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