Detailed view for LmjF.23.1330

Basic information

TDR Targets ID: 23482
Leishmania major, DNA polymerase zeta catalytic subunit, putative
Source Database / ID:  TriTrypDB  GeneDB

pI: 7.9518 | Length (AA): 3096 | MW (Da): 329192 | 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

PF00136   DNA polymerase family B

Gene Ontology

Mouse over links to read term descriptions.
GO:0019985   bypass DNA synthesis  
GO:0016035   zeta DNA polymerase complex  
GO:0003887   DNA-directed DNA polymerase activity  
GO:0003677   DNA binding  
GO:0003676   nucleic acid binding  
GO:0000166   nucleotide binding  
GO:0006281   DNA repair  
GO:0006260   DNA replication  

Metabolic Pathways

Global map (KEGG)
DNA replication (KEGG)

Structural information

Modbase 3D models:

There are 11 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
1691 2710 2gv9 (A) 62 1190 21.00 0 1 0.04 0.63
2132 2569 1d5a (A) 250 631 30.00 0 1 0.39 -0.17
726 847 2mqa (A) 18 138 18.00 0 0.18 0.194206 -0.04
1417 1717 4w4i (A) 4 264 20.00 0 0.75 0.00832222 1.45
1427 1615 3wqc (A) 52 244 31.00 0.09 0.53 0.162747 0.99
1847 2697 2gv9 (B) 232 1178 19.00 0 1 0.239571 1.25
1918 2759 4ptf (A) 211 1184 13.00 0 0.92 -0.0193362 1.73
1951 2710 1tgo (A) 98 762 22.00 0 1 0.265178 1.1
2002 2892 5exr (C) 551 1432 17.00 0 1 0.265491 1.32
2280 2589 4fvm (A) 848 1114 32.00 0 1 0.251829 0.56
2826 2895 2cue (A) 8 76 19.00 0.000036 0.04 0.20631 -0.2

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 20-40% percentile amastigotes, metacyclic. 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_128651)

Species Accession Gene Product
Arabidopsis thaliana AT1G67500   DNA polymerase zeta subunit
Arabidopsis thaliana AT1G55040   Zn-finger in Ran binding domain-containing protein
Babesia bovis BBOV_III010120   DNA polymerase family B family protein
Brugia malayi Bm1_09315   DNA polymerase family B containing protein
Candida albicans CaO19.7389   similar to N terminus of S. cerevisiae REV3 (YPL167C) DNA polymerase zeta subunit involved in DNA repair
Candida albicans CaO19.7390   similar to C terminus of S. cerevisiae REV3 (YPL167C) DNA polymerase zeta subunit involved in DNA repair
Caenorhabditis elegans CELE_Y37B11A.2   Protein Y37B11A.2
Dictyostelium discoideum DDB_G0271608   DNA polymerase zeta catalytic subunit
Drosophila melanogaster Dmel_CG1925   mutagen-sensitive 205
Echinococcus granulosus EgrG_000149300   DNA polymerase zeta catalytic subunit
Entamoeba histolytica EHI_068010   DNA polymerase zeta catalytic subunit, putative
Echinococcus multilocularis EmuJ_000149300   DNA polymerase zeta catalytic subunit
Homo sapiens ENSG00000009413   REV3-like, polymerase (DNA directed), zeta, catalytic subunit
Leishmania braziliensis LbrM.23.1450   DNA polymerase zeta catalytic subunit, putative
Leishmania donovani LdBPK_231590.1   DNA polymerase zeta catalytic subunit, putative
Leishmania infantum LinJ.23.1590   DNA polymerase zeta catalytic subunit, putative
Leishmania major LmjF.23.1330   DNA polymerase zeta catalytic subunit, putative
Leishmania mexicana LmxM.23.1330   DNA polymerase zeta catalytic subunit, putative
Loa Loa (eye worm) LOAG_13925   hypothetical protein
Loa Loa (eye worm) LOAG_14745   hypothetical protein
Loa Loa (eye worm) LOAG_11287   hypothetical protein
Loa Loa (eye worm) LOAG_12098   hypothetical protein
Mus musculus ENSMUSG00000019841   REV3-like, catalytic subunit of DNA polymerase zeta RAD54 like (S. cerevisiae)
Neospora caninum NCLIV_040490   DNA polymerase (EC 2.7.7.7), related
Oryza sativa 4342984   Os07g0404300
Onchocerca volvulus OVOC2477   DNA polymerase homolog
Saccharomyces cerevisiae YPL167C   Rev3p
Schistosoma japonicum Sjp_0210840   ko:K02350 DNA polymerase zeta subunit, putative
Schistosoma japonicum Sjp_0210830   expressed protein
Schistosoma mansoni Smp_125680   DNA polymerase zeta catalytic subunit
Schmidtea mediterranea mk4.001967.04  
Schmidtea mediterranea mk4.001967.03   DNA polymerase
Schmidtea mediterranea mk4.001967.02   DNA polymerase
Trypanosoma brucei gambiense Tbg972.8.3050   DNA polymerase zeta catalytic subunit, putative
Trypanosoma brucei Tb927.8.3290   DNA polymerase zeta catalytic subunit, putative
Trypanosoma congolense TcIL3000_8_3340   DNA polymerase zeta catalytic subunit, putative
Trypanosoma cruzi TcCLB.509769.130   DNA polymerase zeta catalytic subunit, putative
Toxoplasma gondii TGME49_264670   DNA polymerase family B protein
Trichomonas vaginalis TVAG_328140   DNA polymerase alpha catalytic subunit, putative

Essentiality

LmjF.23.1330 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.8.3290 Trypanosoma brucei significant gain of fitness in bloodstream forms (3 days) alsford
Tb927.8.3290 Trypanosoma brucei significant gain of fitness in bloodstream forms (6 days) alsford
Tb927.8.3290 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.8.3290 Trypanosoma brucei significant gain of fitness in differentiation of procyclic to bloodstream forms alsford
TGME49_264670 Toxoplasma gondii Essentiality uncertain sidik
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
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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
  • 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): 0.5

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

  • BRENDA Assay
  • An enzyme with this EC number or name or sequence has been assayed in Leishmania mexicana ( 1 )

Reagent availability

  • Reagent:
  • Target Type Source Notes
    LmjF.23.1330 purified protein BRENDA A protein with this EC number or name or sequence has been purified from Leishmania mexicana ( 1 )

Bibliographic References

9 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.

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Gene identifier LmjF.23.1330 (Leishmania major), DNA polymerase zeta catalytic subunit, putative
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