Detailed view for Rv1310

Basic information

TDR Targets ID: 5699
Mycobacterium tuberculosis, Probable ATP synthase beta chain AtpD
Source Database / ID:  Tuberculist 

pI: 4.5971 | Length (AA): 486 | MW (Da): 53094 | Paralog Number: 0

Signal peptide: N | 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

PF00006   ATP synthase alpha/beta family, nucleotide-binding domain
PF00306  
PF02874   ATP synthase alpha/beta family, beta-barrel domain

Gene Ontology

Mouse over links to read term descriptions.
GO:1902600   GO:proton transmembrane transport  

GO:0046933   hydrogen ion transporting ATP synthase activity, rotational mechanism  
GO:0045261   proton-transporting ATP synthase complex, catalytic core F(1)  
GO:0033178   proton-transporting two-sector ATPase complex, catalytic domain  
GO:0016820   hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances  
GO:0016469   proton-transporting two-sector ATPase complex  
GO:0000166   nucleotide binding  
GO:0017111   nucleoside-triphosphatase activity  
GO:0005524   ATP binding  
GO:0046034   ATP metabolic process  
GO:0015992   proton transport  
GO:0015991   ATP hydrolysis coupled proton transport  
GO:0015986   ATP synthesis coupled proton transport  

Metabolic Pathways

Oxidative phosphorylation (KEGG)
Global map (KEGG)

Structural information

Modbase 3D models:

There are 3 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
16 484 3zia (D) 6 475 61.00 0 1 1.76102 -1.03
19 483 1sky (E) 2 470 65.00 0 1 1.78879 -0.89
20 485 6f5d (D) 13 481 56.00 0 1 1.68445 -0.96

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
Lower 0-20% percentile Dormant phase, Dormant phase. hasan murphy
Show/Hide expression data references
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.

Orthologs

Ortholog group members (OG5_127099)

Species Accession Gene Product
Arabidopsis thaliana ArthCp029   ATPase beta chain
Arabidopsis thaliana AT5G08680   ATP synthase subunit beta-3
Arabidopsis thaliana AT5G08690   ATP synthase subunit beta-2
Arabidopsis thaliana AT5G08670   ATP synthase subunit beta-1
Arabidopsis thaliana ArthCp026   NADH dehydrogenase 27 kDa subunit
Babesia bovis BBOV_IV005830   ATP synthase F1 beta chain, putative
Brugia malayi Bm1_45960   ATP synthase beta chain, mitochondrial precursor, putative
Candida albicans CaO19.5653   beta subunit of mitochondrial F1F0-ATPase
Candida albicans CaO19.13098   beta subunit of mitochondrial F1F0-ATPase
Caenorhabditis elegans CELE_C34E10.6   Protein ATP-2
Cryptosporidium hominis Chro.20148   ATP synthase beta chain, mitochondrial precursor
Cryptosporidium parvum cgd2_1360   ATP synthase beta chain, mitochondrial precursor, putative
Chlamydia trachomatis CT_669   type III secretion system ATPase
Dictyostelium discoideum DDB_G0269916   ATP synthase beta chain, mitochondrial
Drosophila melanogaster Dmel_CG11154   ATP synthase-beta
Drosophila melanogaster Dmel_CG5389   male sterile (3) 72Dt
Escherichia coli b3732   F1 sector of membrane-bound ATP synthase, beta subunit
Echinococcus granulosus EgrG_000752000   ATP synthase subunit beta mitochondrial
Echinococcus multilocularis EmuJ_000752000   ATP synthase subunit beta, mitochondrial
Homo sapiens ENSG00000110955   ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide
Leishmania braziliensis LbrM.25.1150   ATPase beta subunit, putative
Leishmania donovani LdBPK_251210.1   ATP synthase subunit beta, mitochondrial, putative
Leishmania infantum LinJ.25.1210   ATPase beta subunit, putative
Leishmania infantum LinJ.25.2580   ATPase beta subunit, putative
Leishmania major LmjF.25.1180   ATPase beta subunit, putative
Leishmania major LmjF.25.1170   ATPase beta subunit, putative
Leishmania mexicana LmxM.25.1170   ATPase beta subunit, putative
Leishmania mexicana LmxM.25.1180  
Loa Loa (eye worm) LOAG_08048   ATP synthase subunit beta
Mycobacterium leprae ML1145   PROBABLE ATP SYNTHASE BETA CHAIN ATPD
Mus musculus ENSMUSG00000025393   ATP synthase, H+ transporting mitochondrial F1 complex, beta subunit
Mycobacterium tuberculosis Rv1310   Probable ATP synthase beta chain AtpD
Mycobacterium ulcerans MUL_3954   F0F1 ATP synthase subunit beta
Neospora caninum NCLIV_025670   ATP synthase subunit beta (EC 3.6.3.14), related
Oryza sativa 4351757   Os12g0207500
Oryza sativa 3131461   ATP synthase epsilon chain
Oryza sativa 3131459   NADH dehydrogenase 27 kDa subunit
Oryza sativa 3131462   ATPase beta chain
Oryza sativa 4324151   Os01g0685800
Oryza sativa 9271553   Os01g0791150
Oryza sativa 4339546   Os05g0553000
Plasmodium berghei PBANKA_1450300   ATP synthase subunit beta, mitochondrial
Plasmodium falciparum PF3D7_1235700   ATP synthase subunit beta, mitochondrial
Plasmodium knowlesi PKNH_1455400   ATP synthase subunit beta, mitochondrial, putative
Plasmodium vivax PVX_100735   ATP synthase subunit beta, mitochondrial, putative
Plasmodium yoelii PY00963   ATP synthase F1, beta subunit
Saccharomyces cerevisiae YJR121W   F1F0 ATP synthase subunit beta
Schistosoma japonicum Sjp_0059730   ko:K01549 ATP synthase [EC3.6.3.14], putative
Schistosoma mansoni Smp_038100   ATP synthase beta subunit
Schmidtea mediterranea mk4.001599.04   ATP synthase subunit beta, mitochondrial
Trypanosoma brucei gambiense Tbg972.3.1130   ATP synthase beta chain, mitochondrial precursor,ATP synthase F1, beta subunit
Trypanosoma brucei Tb927.3.1380   ATP synthase subunit beta, mitochondrial
Trypanosoma cruzi TcCLB.509233.180   ATP synthase subunit beta, mitochondrial, putative
Toxoplasma gondii TGME49_261950   ATP synthase beta subunit ATP-B
Treponema pallidum TP0402   flagellum-specific ATP synthase (fliI)
Theileria parva TP01_0389   ATP synthase F1, beta chain, putative
Wolbachia endosymbiont of Brugia malayi Wbm0689   ATP synthase F0F1 subunit beta

Essentiality

Rv1310 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu1332 this record Mycobacterium tuberculosis essential nmpdr
Tb927.3.1380 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.3.1380 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.3.1380 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.3.1380 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b3732 Escherichia coli non-essential goodall
CELE_C34E10.6 Caenorhabditis elegans embryonic lethal wormbase
CELE_C34E10.6 Caenorhabditis elegans larval arrest wormbase
CELE_C34E10.6 Caenorhabditis elegans slow growth wormbase
CELE_C34E10.6 Caenorhabditis elegans sterile wormbase
PBANKA_1450300 Plasmodium berghei Slow plasmo
TGME49_261950 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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.
  • 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.
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
growth (GO:0040007) lethal (sensu genetics) (PATO:0000718) inferred from loss-of-function mutant phenotype (ECO:0000016) Mycobacterium smegmatis No drug identifiers listed for this gene.
Annotator: crowther@u.washington.edu. Comment: 2008-01-02. References: 15995221

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): 0.7

Known modulators for this target

Compound Source Reference
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Predicted associations

By orthology with druggable targets
Species Known druggable target Linked compounds Reference
Saccharomyces cerevisiae F1F0 ATP synthase subunit beta 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
0.0087 0.2699 0.5
0.0032 0.9108 1
0.0213 0.7157 1
0.004 1 1
0.0085 0.3625 1
0.0079 0.3283 0.5
0.0336 0.764 1
0.0223 0.9779 0.9773
0.0056 0.4835 0.5
0.0301 0.3562 1
0.008 0.3271 0.5
0.0077 0.2654 0.5
0.0164 0.3045 1
0.013 1 1
0.0264 0.3155 1
0.0073 0.3229 0.5
0.0129 0.2609 1
0.0263 0.282 1
0.0064 0.4392 0.3825
0.0087 0.2689 0.5
0.01 0.307 0.307
0.0263 0.3106 1
0.0079 0.3283 0.5
0.0085 0.3625 1
0.0044 0.6052 1
0.0332 0.6996 1
0.0088 0.2905 0.5

Assayability

Assay information

  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis ATP synthase
  • ChEMBL
  • Inhibition of Mycobacterium tuberculosis H37Rv ATP synthase assessed as reduction in total ATP content at 100 uM after 18 hrs by bead-vortexing settling method

Reagent availability

  • Reagent:
  • Target Type Source Notes
    Rv1310 purified protein BRENDA A protein with this EC number or name or sequence has been purified from Mycobacterium phlei ( 1 )

Bibliographic References

15 literature references were collected for this gene.

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Gene identifier Rv1310 (Mycobacterium tuberculosis), Probable ATP synthase beta chain AtpD
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