Detailed view for Rv3809c

Basic information

TDR Targets ID: 6140
Mycobacterium tuberculosis, UDP-galactopyranose mutase Glf (UDP-GALP mutase) (NAD+-flavin adenine dinucleotide-requiring enzyme)

Source Database / ID:  Tuberculist 

pI: 5.596 | Length (AA): 399 | MW (Da): 45814 | Paralog Number: 0

Signal peptide: N | GPI Anchor: | 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

PF03275   UDP-galactopyranose mutase
PF13450   NAD(P)-binding Rossmann-like domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0016491   oxidoreductase activity  
GO:0008767   UDP-galactopyranose mutase activity  
GO:0005488   binding  
GO:0003824   catalytic activity  
GO:0008152   metabolic process  

Structural information

Modbase 3D models:

There is 1 model calculated for this protein. More info on this model, including the model itself is available at: Modbase

Target Beg Target End Template Template Beg Template End Identity Evalue Model Score MPQS zDope
5 397 5er9 (A) 14 406 86.00 0 1 2.07046 -1.31

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:

  • 1V0J:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 4RPG:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 4RPH:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 4RPJ:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 4RPK:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
  • 4RPL:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Dormant phase. murphy
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile Dormant phase. hasan
Show/Hide expression data references
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.

Orthologs

Ortholog group members (OG5_139595)

Species Accession Gene Product
Escherichia coli b2036   UDP-galactopyranose mutase, FAD/NAD(P)-binding
Mycobacterium leprae ML0092   Probable UDP-galactopyranose mutase Glf (UDP-galp mutase) (NAD+-flavin adenine dinucleotide-requiring enzyme)
Mycobacterium tuberculosis Rv3809c   UDP-galactopyranose mutase Glf (UDP-GALP mutase) (NAD+-flavin adenine dinucleotide-requiring enzyme)
Mycobacterium ulcerans MUL_4993   UDP-galactopyranose mutase Glf
Schmidtea mediterranea mk4.077196.01  

Essentiality

Rv3809c has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu3876 this record Mycobacterium tuberculosis non-essential nmpdr
b2036 Escherichia coli non-essential goodall
Show/Hide essentiality data references
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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.
  • 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.
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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
  • 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
  • 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
  • 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)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
catalytic activity (GO:0003824) decreased (PATO:0000468) in vitro (MI:0492) inferred from specific protein inhibition (ECO:0000020) Mycobacterium tuberculosis 0  
Annotator: crowther@u.washington.edu. Comment: 2007-12-31. References: 12499218

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): 0.2


Known modulators for this target

Compound Source Reference
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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

Ranking Plot


Putative Drugs List


Compound Raw Global Species
0.0688 0.8538 0.5
0.0562 0.406 1
0.1906 0.5219 1
0.0568 0.2709 0.6406
0.0688 1 1
0.1812 1 1
0.0552 0.4045 0.6636
0.3867 0.507 1
0.055 0.2551 0.7729
0.057 0.3441 1
0.1724 1 1
0.0592 0.4237 0.7256
0.1787 0.4325 1
0.0564 0.4055 0.707
0.0552 0.4045 0.6636
0.0565 0.4142 1
0.1114 0.4649 1
0.1821 1 1
0.0562 0.262 0.7427
0.0632 0.5898 1
0.131 0.4175 1
0.0582 0.9602 1
0.1812 1 1
0.0565 0.4043 0.6535
0.1279 0.3883 1
0.0579 0.3499 1
0.0558 0.404 0.6784
0.1885 0.7632 1
0.0582 0.6117 1
0.0558 0.3818 1
0.0565 0.4042 0.6285
0.1161 0.5466 1
0.0674 1 1
0.0579 0.2704 0.6154
0.1122 0.8985 1
0.0607 0.4083 0.8984
0.0573 1 1
0.1129 0.6661 1
0.0553 0.4068 0.6534
0.057 0.616 1
0.1836 0.5096 1
0.1162 0.3995 1
0.0595 0.6599 1
0.0656 0.6029 1
0.0579 0.4371 1
0.174 0.3366 1
0.1839 0.6088 1
0.1135 0.404 1
0.0587 0.592 1
0.0564 1 1
0.0595 0.4915 1
0.0574 1 1
0.0588 0.2733 0.7161
0.0569 0.6592 1
0.0567 0.5761 1
0.1142 0.7138 1
0.0688 0.321 1
0.0572 0.7076 1
0.174 0.3366 1
0.0553 0.4073 0.6792
0.056 0.4051 0.6731
0.0565 0.4044 0.617
0.3867 0.507 1
0.2344 1 1
0.1306 0.3899 1
0.0561 0.6685 1
0.055 1 1
0.1164 0.4039 1
0.1198 0.566 1
0.1203 0.4498 1
0.0588 0.2806 1
0.0654 0.5345 1
0.0557 0.7032 1
0.0629 1 1
0.056 0.4051 0.6176
0.0512 0.4304 1
0.0571 0.4032 1
0.0740666 1 1
0.1818 0.7009 1
0.0688 1 1
0.0688 0.8237 1
0.0559 0.4073 0.878
0.0575 0.6988 1
0.0558 0.3818 1
0.055 0.4039 0.6034
0.0688 0.8314 1
0.0555 0.7956 1
0.0688 0.7011 1
0.0555 0.2532 0.7668
0.055 0.5576 1
0.0654 0.5345 1
0.0587 0.5141 1
0.0688 1 1
0.0582 0.6117 1
0.0575 0.7281 1
0.0579 0.6616 1
0.0556 0.4049 0.6642
0.0553 0.3689 1
0.0582 0.6117 1
0.1745 1 1
0.0568 0.2704 0.6278
0.0674 0.7341 1
0.1245 1 1
0.0688 1 1
0.0562 0.262 0.7427
0.1134 0.4003 1
0.1705 0.6887 1
0.1173 0.5544 1
0.1297 0.7213 1
0.112 0.2641 0.6508
0.182 0.7321 1
0.0553 0.6536 1
0.0688 1 1
0.0561 0.4043 0.6718
0.1735 1 1
0.0566 0.4089 1
0.0654 1 1
0.1142 0.7138 1
0.0622 0.8237 1
0.3867 0.507 1
0.0551 0.2708 1
0.0556 0.652 1
0.1198 0.4754 1
0.0688 1 1
0.0557 0.3149 0.3137
0.118 0.3056 1
0.0578 0.6151 1
0.056 0.3491 1
0.0665 0.7094 1
0.0629 1 1
0.0557 0.3149 0.3137
0.112 0.2641 0.6508
0.1787 0.4325 1
0.055 0.6147 1
0.0559 0.4073 0.878
0.0614 0.3298 0.3289
0.0667 0.502 1
0.0688 1 1
0.0565 0.4043 0.6535
0.0615 0.3363 1
0.0561 0.6992 1
0.1835 0.4223 1
0.0551 0.3316 1
0.0611 0.6833 1
0.0563 0.4042 0.6165
0.0559 0.4622 0.9969
0.0631 1 1
0.0556 0.3487 1
0.0407 0.386 0.4886
0.0642 0.7146 1
0.1111 1 1
0.0553 0.4164 1
0.1804 0.312 1
0.0554 0.3743 1
0.0552 0.6237 1
0.0688 0.8238 1
0.0589 0.8225 1
0.1818 1 1
0.0643 0.2681 0.8814
0.059 0.6741 1
0.1818 0.5097 1
0.0688 0.8229 1
0.174 0.3366 1
0.156 0.3288 1
0.0629 1 1
0.0668 0.3499 0.8821
0.0688 0.8245 1
0.0555 0.6588 1
0.0809 0.2968 1
0.0372 0.3193 1
0.0564 0.4055 0.707
0.0555 0.4047 0.6787
0.0583 0.7088 1
0.0596 0.6992 0.5
0.0567 0.9609 1
0.0563 0.5926 0.938
0.0688 1 1
0.0688 1 1
0.064 0.3364 1
0.1734 1 1
0.1181 0.4434 1
0.169 1 1
0.055 0.6989 1
0.0585 0.5164 1
0.055 0.4051 0.6661
0.171 0.9144 1
0.0567 0.3531 1
0.0372 0.3193 1
0.1143 0.7013 1
0.0608 1 1
0.0562 0.2728 0.8044
0.1305 1 1
0.0558 0.4694 1
0.0647 1 1
0.0587 1 1
0.1143 0.4004 1
0.0688 0.6992 0.5
0.1264 0.4791 1
0.0585 0.2733 0.7158
0.0629 0.744 1
0.0556 1 1
0.0688 1 1
0.0563 0.4056 1
0.063 0.3577 1
0.0558 0.4047 0.666
0.0573 0.2704 1
0.0628 0.2867 0.3292
0.0639 0.7622 1
0.1229 0.3621 1
0.1327 0.3695 1
0.0612 1 1
0.0556 0.2588 0.5758
0.1742 0.5226 1
0.132 0.3942 1
0.0583 0.3569 1
0.0558 0.2701 0.8197
0.1812 1 1
0.0688 0.8242 1
0.0615 0.3363 1
0.0631 1 1
0.2344 1 1
0.0564 0.6148 1
0.0576 0.2704 0.61
0.0571 0.271 0.6469
0.0553 0.3414 1
0.0729 0.2958 1
0.0557 0.3333 1
0.055 0.4039 0.6034
0.0611 0.673 1
0.0555 1 1
0.0582 0.6117 1
0.1142 0.7016 1
0.0562 0.262 0.7427
0.3867 0.507 1
0.1922 0.5909 1
0.1812 1 1
0.0579 0.2723 0.6164
0.0558 0.3233 0.3201
0.1139 0.4686 1
0.0595 0.4915 1
0.0581 0.6987 1
0.0561 0.6136 1
0.0576 0.6988 1
0.156 0.3288 1
0.0555 0.4051 0.6175
0.0563 0.4042 1
0.0688 1 1
0.174 0.3366 1
0.0688 1 1
0.1735 1 1
0.156 0.3288 1
0.0609 0.8229 1
0.0688 0.7 1
0.1708 1 1
0.055 0.3279 1
0.0556 0.2698 0.8088
0.0557 0.7032 1
0.112 0.2641 0.6508
0.0555 0.7956 1
0.0596 0.6992 0.5
0.0552 1 1
0.1294 0.7098 1
0.0567 0.2744 1
0.0688 0.4178 1
0.0612 1 1
0.0688 0.4504 1
0.0541 0.3381 1
0.0571 0.4094 1
0.3867 0.507 1
0.1113 0.7008 1
0.1132 0.3962 1
0.0566 0.408 1
0.0564 0.4055 0.707
0.0589 0.8221 1
0.0622 0.7751 1
0.0631 1 1
0.0594 0.8221 1
0.0575 0.2714 1
0.0582 0.6117 1
0.0555 0.4047 0.6054
0.1216 0.4789 1
0.174 0.3366 1
0.1165 0.4077 1
0.0654 0.5345 1
0.0576 0.2715 1
0.0688 1 1
0.0565 0.4078 1
0.0544 0.4077 1
0.1198 0.566 1
0.0555 0.7956 1
0.0579 0.8244 1
0.0573 0.2711 0.6597
0.0611 0.673 1
0.055 0.6379 1
0.0688 0.8222 1
0.0583 0.7088 1
0.0559 0.4073 0.878
0.1742 0.5226 1
0.0688 0.824 1
0.0564 0.2899 0.5943
0.1216 0.4789 1
0.0553 0.4068 0.6534
0.1264 0.4778 1
0.1113 0.7008 1
0.0557 0.3149 0.3137
0.0557 0.3149 0.3137
0.0608 0.3308 0.3298
0.0688 0.5417 1
0.0651 0.3501 0.8815
0.0588 0.3436 1
0.1141 0.5378 1
0.1174 0.7007 1
0.0563 0.5926 0.938
0.0563 0.4056 1
0.0668 0.3501 0.8815
0.0578 1 1
0.0581 0.3253 0.3244
0.055 0.4039 0.6034
0.1112 0.3612 1
0.0809 0.2968 1
0.0617 0.3501 0.8815
0.0581 0.2712 0.7155
0.0563 0.7005 1
0.1835 0.4223 1
0.1228 0.4602 1
0.0573 1 1
0.0609 0.984 1
0.1748 1 1
0.1169 0.5519 1
0.0654 0.5345 1
0.1742 0.5226 1
0.064 1 1
0.0671 0.3499 0.8815
0.174 0.3366 1
0.0559 0.2651 0.7816
0.0553 0.6536 1
0.057 0.2716 0.8199
0.1721 1 1
0.0554 1 1
0.0582 0.3556 0.8226
0.0557 0.8593 1
0.156 0.3288 1
0.0633 1 1
0.0629 1 1
0.1263 0.3686 1
0.0551 0.6904 1
0.124 0.4776 1
0.1804 0.312 1
0.0574 0.3252 0.3243
0.0552 0.4057 1

Assayability

Assay information

  • Inhibition of M. tuberculosis UDP-galactose mutase expressed in E. coli UDP-6 [3H]- Galf ChEMBL
  • Inhibition of Mycobacterium tuberculosis UDP-galactose mutase expressed in Escherichia coli UDP-6 [3H]- Galf
  • ChEMBL
  • PUBCHEM_BIOASSAY: Inhibitors of Mycobacterium tuberculosis UDP-galactopyranose mutase (UGM) enzyme Measured in Biochemical System Using Plate Reader - 2105-02_Inhibitor_Dose_CherryPick_Activity. (Class of assay: confirmatory) [Related pubchem assays (depositor defined):AID504439]
  • BRENDA Assay
  • An enzyme with this EC number or name or sequence has been assayed in Mycobacterium tuberculosis ( 1 )

Reagent availability

  • Reagent:
  • Target Type Source Notes
    Rv3809c cloned gene BRENDA A gene with this EC number or name or sequence has been cloned from Mycobacterium tuberculosis ( 1 )

Bibliographic References

15 literature references were collected for this gene.

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Gene identifier Rv3809c (Mycobacterium tuberculosis), UDP-galactopyranose mutase Glf (UDP-GALP mutase) (NAD+-flavin adenine dinucleotide-requiring enzyme)
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