Detailed view for Rv2607

Basic information

TDR Targets ID: 6660
Mycobacterium tuberculosis, Probable pyridoxamine 5'-phosphate oxidase PdxH (PNP/PMP oxidase) (pyridoxinephosphate oxidase) (PNPOX) (pyridoxine 5'-phosphate
Source Database / ID:  Tuberculist 

pI: 5.3833 | Length (AA): 224 | MW (Da): 25186 | Paralog Number: 0

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

PF01243   Pyridoxamine 5'-phosphate oxidase
PF10590   Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region

Gene Ontology

Mouse over links to read term descriptions.
GO:0016638   oxidoreductase activity, acting on the CH-NH2 group of donors  
GO:0048037   cofactor binding  
GO:0010181   FMN binding  
GO:0004733   pyridoxamine-phosphate oxidase activity  
GO:0055114   oxidation reduction  
GO:0008615   pyridoxine biosynthetic process  

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
24 224 2a2j (A) 24 224 99.99 0 1 2.13072 -1.41
42 213 1nrg (A) 59 231 41.00 0 1 1.32026 -0.81

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:

PDB tag
  • 2A2J:
  • 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
  • hasan Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.
  • murphy Identification of gene targets against dormant phase Mycobacterium tuberculosis infections.

Orthologs

Ortholog group members (OG5_129127)

Species Accession Gene Product
Brugia malayi Bm1_26535   pyridoxamine 5'-phosphate oxidase
Candida albicans CaO19.8185   pyridoxine-P-oxidase
Candida albicans CaO19.550   pyridoxine-P-oxidase
Caenorhabditis elegans CELE_F57B9.1   Protein F57B9.1
Dictyostelium discoideum DDB_G0278107   pyridoxamine-5'-phosphate:oxygen oxidoreductase
Drosophila melanogaster Dmel_CG31472   CG31472 gene product from transcript CG31472-RB
Escherichia coli b1638   pyridoxine 5'-phosphate oxidase
Echinococcus granulosus EgrG_000630500   pyridoxine 5' phosphate oxidase
Echinococcus multilocularis EmuJ_000630500   pyridoxine 5' phosphate oxidase
Homo sapiens 55163   pyridoxamine 5'-phosphate oxidase
Loa Loa (eye worm) LOAG_14783   pyridoxamine 5'-phosphate oxidase
Loa Loa (eye worm) LOAG_15658   hypothetical protein
Loa Loa (eye worm) LOAG_13914   pyridoxamine 5'-phosphate oxidase
Mycobacterium leprae ML2131c   PROBABLE PYRIDOXAMINE 5'-PHOSPHATE OXIDASE PDXH (PNP/PMP OXIDASE) (PYRIDOXINEPHOSPHATE OXIDASE) (PNPOX) (PYRIDOXINE 5'-PHOSPHATE
Mus musculus ENSMUSG00000018659   pyridoxine 5'-phosphate oxidase
Mycobacterium tuberculosis Rv2607   Probable pyridoxamine 5'-phosphate oxidase PdxH (PNP/PMP oxidase) (pyridoxinephosphate oxidase) (PNPOX) (pyridoxine 5'-phosphate
Mycobacterium ulcerans MUL_0257   pyridoxamine 5'-phosphate oxidase PdxH
Saccharomyces cerevisiae YBR035C   pyridoxamine-phosphate oxidase PDX3
Schistosoma japonicum Sjp_0068470   ko:K00275 pyridoxamine 5'-phosphate oxidase [EC1.4.3.5], putative
Schistosoma mansoni Smp_051550.2   pyridoxamine 5'-phosphate oxidase
Schmidtea mediterranea mk4.002833.01  
Schmidtea mediterranea mk4.002833.03   Pyridoxine-5'-phosphate oxidase
Schmidtea mediterranea mk4.002833.00   Pyridoxine-5'-phosphate oxidase
Schmidtea mediterranea mk4.026448.00   Pyridoxine-5'-phosphate oxidase
Schmidtea mediterranea mk4.034998.05   AT28215p

Essentiality

Rv2607 has direct evidence of essentiality
Gene/Ortholog Organism Phenotype Source Study
mtu2652 this record Mycobacterium tuberculosis non-essential nmpdr
b1638 Escherichia coli essential goodall
Show/Hide essentiality data references
  • 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
  • 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.
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924

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 pyridoxamine 5'-phosphate oxidase Compounds References
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

3 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.

User comments

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Gene identifier Rv2607 (Mycobacterium tuberculosis), Probable pyridoxamine 5'-phosphate oxidase PdxH (PNP/PMP oxidase) (pyridoxinephosphate oxidase) (PNPOX) (pyridoxine 5'-phosphate
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