Detailed view for TP0889

Basic information

TDR Targets ID: 596325
Treponema pallidum, tRNA pseudouridine 55 synthase (truB)
Source Database / ID:  KEGG  

pI: 9.2608 | Length (AA): 366 | MW (Da): 39471 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | 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

PF01509   TruB family pseudouridylate synthase (N terminal domain)
PF16198   tRNA pseudouridylate synthase B C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0009982   pseudouridine synthase activity  
GO:0003723   RNA binding  
GO:0009451   RNA modification  
GO:0006396   RNA processing  
GO:0001522   pseudouridine synthesis  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in 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
6 365 1ze2 (B) 1 308 33.00 0 1 0.549907 1.84
7 366 1k8w (A) 11 311 26.00 0 0.95 1.00191 1.27
10 238 1sgv (A) 8 218 39.00 0 0.91 0.730283 1.18

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

No expression data available for this gene

Orthologs

Ortholog group members (OG5_126700)

Species Accession Gene Product
Arabidopsis thaliana AT5G14460   pseudouridine synthase family protein
Arabidopsis thaliana AT3G57150   putative pseudouridine synthase NAP57
Babesia bovis BBOV_II005520   rRNA pseudouridine synthase, putative family protein
Babesia bovis BBOV_III005720   tRNA pseudouridine synthase, putative
Brugia malayi Bm1_44720   Nucleolar protein K01G5.5
Candida albicans CaO19.1833   likely pseudouridylate synthase similar to S. cerevisiae box H/ACA snoRNP component CBF5 (YLR175W) involved in nucleolar RNA mod
Candida albicans CaO19.1954   Pseudouridine synthase
Candida albicans CaO19.9391   likely pseudouridylate synthase similar to S. cerevisiae box H/ACA snoRNP component CBF5 (YLR175W) involved in nucleolar RNA mod
Candida albicans CaO19.9509   Pseudouridine synthase
Caenorhabditis elegans CELE_K01G5.5   Protein K01G5.5
Cryptosporidium hominis Chro.30435   hypothetical protein
Cryptosporidium parvum cgd3_3850   Cbf5p; centromere-binding factor 5 like PUA domain containing protein with a type I pseudouridine synthase domain
Chlamydia trachomatis CT_094   tRNA pseudouridine synthase B
Dictyostelium discoideum DDB_G0281933   DKCLD domain-containing protein
Drosophila melanogaster Dmel_CG3333   Nucleolar protein at 60B
Escherichia coli b3166   tRNA pseudouridine synthase B: tRNA pseudouridine(55) synthase and putative tmRNA pseudouridine(342) synthase
Echinococcus granulosus EgrG_000063500   dyskeratosis congenita 1 dyskerin
Entamoeba histolytica EHI_115300   centromere/microtubule binding protein cbf5, putative
Echinococcus multilocularis EmuJ_000063500   dyskeratosis congenita 1, dyskerin
Giardia lamblia GL50803_16311   Centromere/microtubule binding protein CBF5
Homo sapiens ENSG00000165832   TruB pseudouridine (psi) synthase family member 1
Homo sapiens ENSG00000130826   dyskeratosis congenita 1, dyskerin
Leishmania braziliensis LbrM.21.2070   centromere/microtubule binding protein cbf5, putative
Leishmania donovani LdBPK_212130.1   centromere/microtubule binding protein cbf5, putative
Leishmania infantum LinJ.21.2130   centromere/microtubule binding protein cbf5, putative
Leishmania major LmjF.21.1760   centromere/microtubule binding protein cbf5, putative
Leishmania mexicana LmxM.21.1760   centromere/microtubule binding protein cbf5, putative
Loa Loa (eye worm) LOAG_08003   nucleolar protein
Mycobacterium leprae ML1546c   PROBABLE TRNA PSEUDOURIDINE SYNTHASE B TRUB (TRNA PSEUDOURIDINE 55 SYNTHASE) (PSI55 SYNTHASE) (PSEUDOURIDYLATE SYNTHASE) (URACIL
Mus musculus ENSMUSG00000025086   TruB pseudouridine (psi) synthase homolog 1 (E. coli)
Mus musculus ENSMUSG00000031403   dyskeratosis congenita 1, dyskerin
Mycobacterium tuberculosis Rv2793c   Probable tRNA pseudouridine synthase B TruB (tRNA pseudouridine 55 synthase) (PSI55 synthase) (pseudouridylate synthase) (uracil
Mycobacterium ulcerans MUL_2142   tRNA pseudouridine synthase B
Neospora caninum NCLIV_051450   centromere/microtubule binding protein, putative
Neospora caninum NCLIV_044710   tRNA pseudouridine synthase B, putative
Oryza sativa 4344029   Os07g0636000
Oryza sativa 4337577   Os05g0108000
Oryza sativa 4332935   Os03g0370500
Onchocerca volvulus OVOC8566   Putative H\/ACA ribonucleoprotein complex subunit 4
Plasmodium berghei PBANKA_0502300   tRNA pseudouridine synthase, putative
Plasmodium berghei PBANKA_1025200   H/ACA ribonucleoprotein complex subunit 4, putative
Plasmodium falciparum PF3D7_1417500   H/ACA ribonucleoprotein complex subunit 4, putative
Plasmodium falciparum PF3D7_1018000   tRNA pseudouridine synthase, putative
Plasmodium knowlesi PKNH_0602200   tRNA pseudouridine synthase, putative
Plasmodium knowlesi PKNH_1340500   H/ACA ribonucleoprotein complex subunit 4, putative
Plasmodium vivax PVX_001765   tRNA pseudouridine synthase, putative
Plasmodium vivax PVX_085575   H/ACA ribonucleoprotein complex subunit 4, putative
Plasmodium yoelii PY05447   unknown protein-related
Plasmodium yoelii PY02644   TruB family pseudouridylate synthase, putative
Plasmodium yoelii PY02575   tRNA-pseudouridine synthase B-related
Saccharomyces cerevisiae YLR175W   pseudouridine synthase CBF5
Saccharomyces cerevisiae YNL292W   pseudouridine synthase PUS4
Schistosoma japonicum Sjp_0302000   ko:K01855 DKC1, DKC; dyskeratosis congenita 1, dyskerin [EC:5.4.99.-], putative
Schistosoma mansoni Smp_068920.1   centromere/microtubule binding protein cbf5
Schistosoma mansoni Smp_068920.3   centromere/microtubule binding protein cbf5
Schistosoma mansoni Smp_068920.2   centromere/microtubule binding protein cbf5
Schmidtea mediterranea mk4.011526.00   Putative centromere/microtubule binding protein cbf5
Trypanosoma brucei gambiense Tbg972.10.80   centromere/microtubule binding protein cbf5, putative
Trypanosoma brucei Tb927.10.170   pseudouridine synthase, Cbf5p
Trypanosoma congolense TcIL3000_10_40   centromere/microtubule binding protein cbf5, putative
Trypanosoma cruzi TcCLB.504069.90   centromere/microtubule binding protein cbf5, putative
Trypanosoma cruzi TcCLB.511145.70   centromere/microtubule binding protein cbf5, putative
Toxoplasma gondii TGME49_214210   rRNA pseudouridine synthase
Treponema pallidum TP0889   tRNA pseudouridine 55 synthase (truB)
Theileria parva TP02_0380   tRNA pseudouridine synthase, putative
Theileria parva TP02_0508   rRNA pseudouridine synthase, putative
Trichomonas vaginalis TVAG_407130   centromere/microtubule binding protein cbf5, putative

Essentiality

TP0889 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.170 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb927.10.170 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (6 days) alsford
Tb927.10.170 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb927.10.170 Trypanosoma brucei no significant loss or gain of fitness in differentiation of procyclic to bloodstream forms alsford
b3166 Escherichia coli non-essential goodall
CELE_K01G5.5 Caenorhabditis elegans larval arrest wormbase
CELE_K01G5.5 Caenorhabditis elegans slow growth wormbase
YLR175W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0502300 Plasmodium berghei Dispensable plasmo
PBANKA_1025200 Plasmodium berghei Essential plasmo
TGME49_214210 Toxoplasma gondii Probably essential sidik
TGME49_214210 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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
  • 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • 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.
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs

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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Gene identifier TP0889 (Treponema pallidum), tRNA pseudouridine 55 synthase (truB)
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