Detailed view for Rv0570

Basic information

TDR Targets ID: 981487
Mycobacterium tuberculosis, Probable ribonucleoside-diphosphate reductase (large subunit) NrdZ (ribonucleotide reductase)

Source Database / ID:  Tuberculist 

pI: 7.9258 | Length (AA): 692 | MW (Da): 74489 | Paralog Number: 1

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

No Pfam domain information for this protein.

Gene Ontology

Mouse over links to read term descriptions.
No GO information for this protein.

Metabolic Pathways

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
6 680 1zyz (A) 36 767 27.00 0 1 1.19503 -0.02
106 659 3o0q (A) 12 632 43.00 0 1 1.26218 -0.7

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_126839)

Species Accession Gene Product
Arabidopsis thaliana AT2G21790   ribonucleoside-diphosphate reductase large subunit
Babesia bovis BBOV_I004870   ribonucleoside-diphosphate reductase large chain
Brugia malayi Bm1_17945   ribonucleoside-diphosphate reductase large chain, putative
Candida albicans CaO19.13267   one of two likely ribonucleotide reductase large subunit genes similar to S. cerevisiae RNR1 (YER070W) and RNR3 (YIL066C)
Candida albicans CaO19.13201   one of two likely ribonucleotide reductase large subunit genes similar to S. cerevisiae RNR1 (YER070W) and RNR3 (YIL066C)
Candida albicans CaO19.5779   one of two likely ribonucleotide reductase large subunit genes similar to S. cerevisiae RNR1 (YER070W) and RNR3 (YIL066C)
Candida albicans CaO19.5845   one of two likely ribonucleotide reductase large subunit genes similar to S. cerevisiae RNR1 (YER070W) and RNR3 (YIL066C)
Caenorhabditis elegans CELE_T23G5.1   Protein RNR-1
Cryptosporidium hominis Chro.60230   ribonucleoside-diphosphate reductase large chain (ribonucleotide reductase R1 subunit)
Cryptosporidium parvum cgd6_1950   ribonucleotide-diphosphate reductase large chain; RIR1; c-terminal PFL-like glycyl radical enzymes-like fold
Chlamydia trachomatis CT_827   ribonucleoside-diphosphate reductase subunit alpha
Dictyostelium discoideum DDB_G0284071   ribonucleoside-diphosphate reductase
Drosophila melanogaster Dmel_CG5371   Ribonucleoside diphosphate reductase large subunit
Escherichia coli b2234   ribonucleoside-diphosphate reductase 1, alpha subunit
Escherichia coli b2675   ribonucleoside-diphosphate reductase 2, alpha subunit
Echinococcus granulosus EgrG_000823000   ribonucleoside diphosphate reductase large
Echinococcus multilocularis EmuJ_000823000   ribonucleoside diphosphate reductase large
Homo sapiens ENSG00000167325   ribonucleotide reductase M1
Leishmania braziliensis LbrM.28.0960   ribonucleoside-diphosphate reductase large chain, putative
Leishmania donovani LdBPK_280980.1   ribonucleoside-diphosphate reductase large chain, putative
Leishmania infantum LinJ.28.0980   ribonucleoside-diphosphate reductase large chain, putative
Leishmania major LmjF.28.0890   ribonucleoside-diphosphate reductase large chain, putative
Leishmania mexicana LmxM.28.0890   ribonucleoside-diphosphate reductase large chain, putative
Loa Loa (eye worm) LOAG_00652   ribonucleoside-diphosphate reductase large subunit
Mycobacterium leprae ML1734c   RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE (ALPHA CHAIN) NRDE (RIBONUCLEOTIDE REDUCTASE SMALL SUBUNIT) (R1F PROTEIN)
Mus musculus ENSMUSG00000030978   ribonucleotide reductase M1
Mycobacterium tuberculosis Rv3051c   Ribonucleoside-diphosphate reductase (alpha chain) NrdE (ribonucleotide reductase small subunit) (R1F protein)
Mycobacterium tuberculosis Rv0570   Probable ribonucleoside-diphosphate reductase (large subunit) NrdZ (ribonucleotide reductase)
Mycobacterium ulcerans MUL_1878   ribonucleotide-diphosphate reductase subunit alpha
Neospora caninum NCLIV_001550   ribonucleoside-diphosphate reductase, large subunit, putative
Oryza sativa 4340258   Os06g0168600
Oryza sativa 4331059   Os02g0804900
Plasmodium berghei PBANKA_0611600   ribonucleoside-diphosphate reductase large subunit, putative
Plasmodium falciparum PF3D7_1437200   ribonucleoside-diphosphate reductase large subunit, putative
Plasmodium knowlesi PKNH_0423900   ribonucleoside-diphosphate reductase large subunit, putative
Plasmodium vivax PVX_084685   ribonucleoside-diphosphate reductase large chain, putative
Plasmodium yoelii PY03473   ribonucleoside-diphosphate reductase large chain
Saccharomyces cerevisiae YER070W   ribonucleotide-diphosphate reductase subunit RNR1
Saccharomyces cerevisiae YIL066C   ribonucleotide-diphosphate reductase subunit RNR3
Schistosoma japonicum Sjp_0068740   ko:K00525 ribonucleoside-diphosphate reductase alpha chain [EC1.17.4.1A], putative
Schistosoma mansoni Smp_009030   ribonucleoside-diphosphate reductase alpha subunit
Schmidtea mediterranea mk4.006528.00   Ribonucleoside-diphosphate reductase large subunit
Schmidtea mediterranea mk4.034835.00   Ribonucleoside-diphosphate reductase large subunit
Trypanosoma brucei gambiense Tbg972.11.8940   ribonucleoside-diphosphate reductase large chain
Trypanosoma brucei Tb927.11.7840   ribonucleoside-diphosphate reductase large chain
Trypanosoma congolense TcIL3000_0_44200   ribonucleoside-diphosphate reductase large chain
Trypanosoma congolense TcIL3000.11.8380   ribonucleoside-diphosphate reductase large chain
Trypanosoma cruzi TcCLB.506933.20   ribonucleoside-diphosphate reductase large chain, putative
Toxoplasma gondii TGME49_294640   ribonucleoside-diphosphate reductase large chain
Treponema pallidum TP1008   ribonucleotide-diphosphate reductase subunit alpha
Theileria parva TP03_0528   ribonucleotide-diphosphate reductase large subunit, putative
Trichomonas vaginalis TVAG_402580   ribonucleoside-diphosphate reductase alpha chain, putative
Wolbachia endosymbiont of Brugia malayi Wbm0695   ribonucleotide-diphosphate reductase subunit alpha

Essentiality

Rv0570 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
mtu3104 Mycobacterium tuberculosis essential nmpdr
Tb11.02.5720 Trypanosoma brucei no significant loss or gain of fitness in bloodstream forms (3 days) alsford
Tb11.02.5720 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.02.5720 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.02.5720 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b2234 Escherichia coli essential goodall
b2675 Escherichia coli non-essential goodall
CELE_T23G5.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_T23G5.1 Caenorhabditis elegans larval arrest wormbase
CELE_T23G5.1 Caenorhabditis elegans larval lethal wormbase
CELE_T23G5.1 Caenorhabditis elegans slow growth wormbase
CELE_T23G5.1 Caenorhabditis elegans sterile wormbase
YER070W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0611600 Plasmodium berghei Essential plasmo
TGME49_294640 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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.
  • 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.
  • 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.

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
Species Known druggable target Linked compounds Reference
Homo sapiens ribonucleotide reductase M1 Compounds References
Herpes simplex virus (type 1 / strain 17) Ribonucleoside-diphosphate reductase large chain Compounds References
Mycobacterium tuberculosis Ribonucleoside-diphosphate reductase (alpha chain) NrdE (ribonucleotide reductase small subunit) (R1F protein) Compounds References
Mus musculus ribonucleotide reductase M1 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
0.044 0.2987 0.3225
0.0642 0.3027 0.3491
0.0537 0.3022 0.3536
0.0695 0.3189 0.3052
0.1098 0.2995 0.32
0.0845 0.2963 0.3272
0.0674 0.3266 0.3095
0.0651 0.3058 0.3536
0.0277143 0.269846 0.338202
0.0158 0.2583 0.2132
0.057 0.3073 0.329
0.0575 0.2859 0.3278
0.0526 0.3262 0.3453
0.0683 0.3241 0.3528
0.0705 0.3196 0.3452
0.0845 0.2963 0.3272
0.0828 0.3094 0.355
0.1695 0.3134 0.3536
0.0601 0.2944 0.3492
0.0617 0.3062 0.3372
0.0631 0.2942 0.3313
0.0845 0.2963 0.3272
0.06 0.2514 0.3519
0.0526 0.3262 0.3453
0.0771 0.3026 0.3054
0.0324 0.2589 0.3043
0.0999 0.2831 0.3551
0.0541 0.2885 0.3069
0.0662 0.3086 0.3316
0.0597 0.307 0.3536
0.0145 0.2579 0.0283
0.0845 0.2963 0.3272
0.0762 0.3054 0.3364
0.0271 0.2715 0.3449
0.0145 0.2579 0.0283
0.0536 0.3078 0.3273
0.0551 0.327 0.3081
0.0745 0.3047 0.3541
0.0845 0.2963 0.3272
0.0504 0.2618 0.3493
0.0663 0.2926 0.3328
0.0845 0.2963 0.3272
0.0598 0.3201 0.3052
0.0557 0.3209 0.3089
0.0504 0.2626 0.3506
0.1173 0.3187 0.3569
0.0178 0.2937 0.2623
0.1181 0.3068 0.3517
0.0607 0.3039 0.3561
0.0845 0.2963 0.3272
0.0537 0.3022 0.3536
0.0448 0.3231 0.34
0.0434 0.2996 0.3557
0.0704 0.323 0.3336
0.0512 0.2744 0.3213
0.0716 0.2917 0.3365
0.0597 0.307 0.3536
0.0526 0.3262 0.3453
0.0607 0.3039 0.3561
0.0597 0.307 0.3536
0.0658 0.3029 0.3528
0.0838 0.3104 0.3558
0.0248 0.3176 0.3249
0.0526 0.3262 0.3453
0.0597 0.307 0.3536
0.0859 0.3052 0.3425
0.0129 0.2685 0.3214
0.03 0.3309 0.3504
0.06 0.2514 0.3519
0.0637 0.3096 0.3044
0.0509 0.3111 0.2983
0.0092 0.283 0.2132
0.0755 0.3249 0.3491
0.0821 0.3028 0.3459
0.0679 0.3117 0.2978
0.0528 0.3007 0.3069
0.0845 0.2963 0.3272
0.0681 0.3038 0.3532
0.1137 0.3196 0.3572
0.0909 0.2742 0.3483
0.0178 0.2739 0.29
0.0632 0.295 0.3313
0.0989 0.3157 0.3501
0.0148 0.2774 0.2132
0.0533 0.3014 0.313

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 Rv0570 (Mycobacterium tuberculosis), Probable ribonucleoside-diphosphate reductase (large subunit) NrdZ (ribonucleotide reductase)
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