Detailed view for LmjF.34.3080

Basic information

TDR Targets ID: 26941
Leishmania major, exosome subunit rrp6p homologue, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 6.333 | Length (AA): 742 | MW (Da): 80585 | 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

PF00570   HRDC domain
PF01612   3'-5' exonuclease
PF08066   PMC2NT (NUC016) domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0006139   nucleobase, nucleoside, nucleotide and nucleic acid metabolic process  
GO:0000176   nuclear exosome (RNase complex)  
GO:0005622   intracellular  
GO:0008408   3'-5' exonuclease activity  
GO:0003824   catalytic activity  
GO:0003676   nucleic acid binding  
GO:0000166   nucleotide binding  
GO:0044237   cellular metabolic process  
GO:0006396   RNA processing  

Metabolic Pathways

RNA degradation (KEGG)

Structural information

Modbase 3D models:

There are 5 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
163 523 2hbj (A) 129 509 40.00 0 1 1.01 -1.2
230 617 1yt3 (A) 1 369 19.00 0 1 0.81 -0.7
450 522 1wud (A) 530 602 18.00 0.00000000076 0.76 0.56 -2.18
165 525 4nlc (A) 179 539 67.00 0 1 1.32482 -0.87
223 600 5c0w (K) 204 601 33.00 0 1 0.807134 0.5

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 60-80% percentile metacyclic. Fernandes MC
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile amastigotes. Fernandes MC
Show/Hide expression data references
  • Fernandes MC Dual Transcriptome Profiling of Leishmania-Infected Human Macrophages Reveals Distinct Reprogramming Signatures.

Orthologs

Ortholog group members (OG5_127879)

Species Accession Gene Product
Arabidopsis thaliana AT1G54440   RRP6-like protein 1
Arabidopsis thaliana AT5G35910   exosome complex exonuclease RRP6L2
Babesia bovis BBOV_IV002650   exosome component 10, putative
Brugia malayi Bm1_09560   3'-5' exonuclease family protein
Candida albicans CaO19.7719   likely 3'-5' exonuclease similar to S. cerevisiae RRP6 (YOR001W) nuclear exosome component involved in RNA processing
Candida albicans CaO19.58   likely 3'-5' exonuclease similar to S. cerevisiae RRP6 (YOR001W) nuclear exosome component involved in RNA processing
Caenorhabditis elegans CELE_C14A4.4   Protein CRN-3, isoform A
Cryptosporidium hominis Chro.50386   hypothetical protein
Dictyostelium discoideum DDB_G0271572   3'-5' exonuclease
Drosophila melanogaster Dmel_CG7292   CG7292 gene product from transcript CG7292-RC
Escherichia coli b1804   ribonuclease D
Echinococcus granulosus EgrG_000568100   Helicase RNase D C terminal HRDC domain
Echinococcus granulosus EgrG_002000900   hypothetical protein
Entamoeba histolytica EHI_021400   exosome component 10, putative
Echinococcus multilocularis EmuJ_000567700   3' 5' exonuclease
Echinococcus multilocularis EmuJ_000009300   exosome component 10
Echinococcus multilocularis EmuJ_000568100   Helicase RNase D C terminal, HRDC domain
Homo sapiens ENSG00000171824   exosome component 10
Leishmania braziliensis LbrM.20.2660   exosome subunit rrp6p homologue, putative
Leishmania donovani LdBPK_044330.1   exosome subunit rrp6p homologue putative
Leishmania infantum LinJ.34.4330   exosome subunit rrp6p homologue, putative
Leishmania major LmjF.34.3080   exosome subunit rrp6p homologue, putative
Leishmania mexicana LmxM.33.3080   exosome subunit rrp6p homologue, putative
Loa Loa (eye worm) LOAG_00677   3'-5' exonuclease
Mycobacterium leprae ML1040c   conserved hypothetical protein
Mus musculus ENSMUSG00000017264   exosome component 10
Mycobacterium tuberculosis Rv2681   Conserved hypothetical alanine rich protein
Mycobacterium ulcerans MUL_3315   hypothetical protein
Neospora caninum NCLIV_063640   Ribonuclease D, related
Oryza sativa 4331677   Os03g0157800
Oryza sativa 9270208   Os10g0437200
Saccharomyces cerevisiae YOR001W   Rrp6p
Schistosoma japonicum Sjp_0206770   Exosome component 10, putative
Schistosoma mansoni Smp_131150   polymyositis/scleroderma autoantigen-related
Schmidtea mediterranea mk4.002369.05   Polymyositis/scleroderma autoantigen-related
Schmidtea mediterranea mk4.002369.06   Polymyositis/scleroderma autoantigen-related
Trypanosoma brucei gambiense Tbg972.4.1510   ribosomal RNA processing protein 6, putative
Trypanosoma brucei Tb927.4.1630   ribosomal RNA processing protein 6
Trypanosoma congolense TcIL3000_4_1200   ribosomal RNA processing protein 6, putative
Trypanosoma cruzi TcCLB.504057.110   ribosomal RNA processing protein 6, putative
Toxoplasma gondii TGME49_246970   3'-5' exonuclease domain-containing protein
Trichomonas vaginalis TVAG_197890   conserved hypothetical protein
Trichomonas vaginalis TVAG_283650   hypothetical protein
Trichomonas vaginalis TVAG_053630   conserved hypothetical protein
Wolbachia endosymbiont of Brugia malayi Wbm0258   ribonuclease D

Essentiality

LmjF.34.3080 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu2727 Mycobacterium tuberculosis non-essential nmpdr
Tb927.4.1630 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.4.1630 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.4.1630 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.4.1630 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
CELE_C14A4.4 Caenorhabditis elegans embryonic lethal wormbase
CELE_C14A4.4 Caenorhabditis elegans larval arrest wormbase
CELE_C14A4.4 Caenorhabditis elegans slow growth wormbase
TGME49_246970 Toxoplasma gondii Probably essential sidik
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.
  • 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.
  • 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
  • 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
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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

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.

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User comments

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Gene identifier LmjF.34.3080 (Leishmania major), exosome subunit rrp6p homologue, putative
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