Detailed view for Rv2941

Basic information

TDR Targets ID: 6005
Mycobacterium tuberculosis, Fatty-acid-AMP ligase FadD28 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)

Source Database / ID:  Tuberculist 

pI: 5.0569 | Length (AA): 580 | MW (Da): 62641 | Paralog Number: 8

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

PF00501   AMP-binding enzyme

Gene Ontology

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

Structural information

Modbase 3D models:

There are 2 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
4 459 3e53 (A) 4 459 99.99 0 1 1.97151 -1.65
4 578 5es8 (A) 203 706 22.00 0 1 1.05738 0.45

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:

  • 3E53:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 3T5A:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile Dormant phase. murphy
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Dormant phase. hasan
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_127582)

Species Accession Gene Product
Brugia malayi Bm1_18790   Disco-interacting protein 2 homolog
Candida albicans CaO19.5702   similar to acyl-CoA ligase-like proteins in a variety of plant pathogens and to S. cerevisiae YOR093C
Candida albicans CaO19.13125   similar to acyl-CoA ligase-like proteins in a variety of plant pathogens and to S. cerevisiae YOR093C
Caenorhabditis elegans CELE_F28B3.1   Protein F28B3.1
Drosophila melanogaster Dmel_CG7020   DISCO Interacting Protein 2
Echinococcus granulosus EgrG_000939300   disco interacting protein 2
Echinococcus multilocularis EmuJ_000939300   disco interacting protein 2
Homo sapiens ENSG00000151240   DIP2 disco-interacting protein 2 homolog C (Drosophila)
Homo sapiens ENSG00000160305   DIP2 disco-interacting protein 2 homolog A (Drosophila)
Homo sapiens ENSG00000066084   DIP2 disco-interacting protein 2 homolog B (Drosophila)
Loa Loa (eye worm) LOAG_09084   hypothetical protein
Loa Loa (eye worm) LOAG_12662   hypothetical protein
Mycobacterium leprae ML2358c   FATTY-ACID-CoA LIGASE FADD26 (FATTY-ACID-COA SYNTHETASE) (FATTY-ACID-CoA SYNTHASE)
Mycobacterium leprae ML1234c   PROBABLE FATTY-ACID--CoA LIGASE FADD21 (FATTY-ACID-CoA SYNTHETASE) (FATTY-ACID-CoA SYNTHASE)
Mycobacterium leprae ML0132   Probable fatty-acid-CoA synthetase FadD29 (fatty-acid-CoA ligase) (fatty-acid-CoA synthase)
Mycobacterium leprae ML0138c   Probable fatty-acid-CoA synthetase FadD28 (fatty-acid-CoA ligase) (fatty-acid-CoA synthase)
Mycobacterium leprae ML0100   Probable fatty-acid-CoA synthetase FadD32 (fatty-acid-CoA ligase) (fatty-acid-CoA synthase)
Mus musculus ENSMUSG00000020231   DIP2 disco-interacting protein 2 homolog A (Drosophila)
Mus musculus ENSMUSG00000048264   DIP2 disco-interacting protein 2 homolog C (Drosophila)
Mus musculus ENSMUSG00000023026   DIP2 disco-interacting protein 2 homolog B (Drosophila)
Mycobacterium tuberculosis Rv1529   Probable fatty-acid-AMP ligase FadD24 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)
Mycobacterium tuberculosis Rv1185c   Probable fatty-acid-AMP ligase FadD21 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)
Mycobacterium tuberculosis Rv3826   Probable fatty-acid-AMP ligase FadD23 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)
Mycobacterium tuberculosis Rv1521   Probable fatty-acid-AMP ligase FadD25 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)
Mycobacterium tuberculosis Rv2930   Fatty-acid-AMP ligase FadD26 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)
Mycobacterium tuberculosis Rv2941   Fatty-acid-AMP ligase FadD28 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)
Mycobacterium tuberculosis Rv2950c   Fatty-acid-AMP ligase FadD29 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)
Mycobacterium tuberculosis Rv1925   Probable acyl-CoA ligase FadD31 (acyl-CoA synthetase) (acyl-CoA synthase)
Mycobacterium tuberculosis Rv3801c   Fatty-acid-AMP ligase FadD32 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase). Also shown to have acyl-ACP ligase activity.
Mycobacterium ulcerans MUL_4984   long-chain-fatty-acid--CoA ligase
Mycobacterium ulcerans MUL_1432   acyl-CoA synthetase
Mycobacterium ulcerans MUL_2008   acyl-CoA synthetase
Mycobacterium ulcerans MUL_1117   fatty-acid-CoA ligase
Mycobacterium ulcerans MUL_2920   putative fatty-acid--CoA ligase
Mycobacterium ulcerans MUL_2002   acyl-CoA synthetase
Mycobacterium ulcerans MUL_2020   acyl-CoA synthetase
Oryza sativa 9266980   Os04g0473900
Oryza sativa 4339712   Os05g0579200
Saccharomyces cerevisiae YOR093C   hypothetical protein
Schistosoma japonicum Sjp_0089700   Disco-interacting protein 2 homolog B, putative
Schistosoma mansoni Smp_051610   disco-interacting protein 2 (dip2)
Schmidtea mediterranea mk4.007525.03   Disco-interacting protein 2
Schmidtea mediterranea mk4.007525.00   Disco-interacting protein 2
Schmidtea mediterranea mk4.007525.04   Disco-interacting protein 2
Schmidtea mediterranea mk4.000169.02  
Schmidtea mediterranea mk4.000169.01   Disco-interacting protein 2
Schmidtea mediterranea mk4.027630.01   Disco-interacting protein 2
Schmidtea mediterranea mk4.027630.00   Disco-interacting protein 2
Schmidtea mediterranea mk4.007525.01   Disco-interacting protein 2

Essentiality

Rv2941 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu1206 Mycobacterium tuberculosis non-essential nmpdr
mtu1549 Mycobacterium tuberculosis non-essential nmpdr
mtu2978 Mycobacterium tuberculosis non-essential nmpdr
mtu2999 Mycobacterium tuberculosis non-essential nmpdr
mtu1956 Mycobacterium tuberculosis non-essential nmpdr
mtu3868 Mycobacterium tuberculosis essential nmpdr
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.
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924

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

62 chemical compounds are associated with this gene

Predicted associations

By orthology with druggable targets
Non orthologous druggable targets
By sequence similarity to non orthologous druggable targets
Species Target Length Identity Alignment span Linked Drugs Reference
Photuris pennsylvanica Luciferase 552 aa 20.6% 467 aa Compounds References
Photinus pyralis Luciferin 4-monooxygenase 550 aa 22.6% 504 aa Compounds References
Photuris pennsylvanica Luciferin 4-monooxygenase 545 aa 21.6% 473 aa Compounds References
Luciola lateralis Luciferase 548 aa 22.0% 490 aa Compounds References
Yersinia pestis AMP-binding enzyme family protein 525 aa 22.5% 489 aa Compounds References

Obtained from network model
No druggable targets predicted through repurposing network model

Assayability

Assay information

  • ChEMBL
  • PubChem BioAssay. Fluorescence polarization aasay to screen for inhibitors that compete for the binding of FadD28 to a bisubstrate Measured in Biochemical System Using Plate Reader - 2147-01_Inhibitor_Dose_CherryPick_Activity. (Class of assay: confirmatory)
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis FadD28 expressed in Escherichia coli at 100 uM
  • BRENDA Assay
  • An enzyme with this EC number or name or sequence has been assayed in Mycobacterium tuberculosis ( 1 )

Reagent availability

  • Reagent:
  • Target Type Source Notes
    Rv2941 cloned gene BRENDA A gene with this EC number or name or sequence has been cloned from Mycobacterium tuberculosis ( 2 )

Bibliographic References

12 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.

User comments

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

Enter your comment

User ()
Gene identifier Rv2941 (Mycobacterium tuberculosis), Fatty-acid-AMP ligase FadD28 (fatty-acid-AMP synthetase) (fatty-acid-AMP synthase)
Title for this comment
Comment