Detailed view for LmjF.36.6650

Basic information

TDR Targets ID: 28486
Leishmania major, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Source Database / ID:  TriTrypDB  GeneDB

pI: 5.0701 | Length (AA): 553 | MW (Da): 60713 | 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

PF01676   Metalloenzyme superfamily
PF06415   BPG-independent PGAM N-terminus (iPGM_N)

Gene Ontology

Mouse over links to read term descriptions.
GO:0005737   cytoplasm  
GO:0004619   phosphoglycerate mutase activity  
GO:0003824   catalytic activity  
GO:0046872   metal ion binding  
GO:0030145   manganese ion binding  
GO:0008152   metabolic process  
GO:0006007   glucose catabolic 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
13 550 1o98 (A) 2 509 34.00 0 1 1.38 -1.08
4 552 3igz (B) 4 552 92.00 0 1 2.16417 -1.59

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
  • 3IGY:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date
PDB tag
  • 3IGZ:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 60-80% 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_129051)

Species Accession Gene Product
Arabidopsis thaliana AT3G08590   phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent
Arabidopsis thaliana AT1G09780   2,3-bisphosphoglycerate-independent phosphoglycerate mutase 1
Brugia malayi Bm1_04665   2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Caenorhabditis elegans CELE_F57B10.3   Protein F57B10.3, isoform B
Escherichia coli b3612   phosphoglycero mutase III, cofactor-independent
Entamoeba histolytica EHI_050940   2,3-bisphosphoglycerate-independent phosphoglycerate mutase, putative
Giardia lamblia GL50803_8822   2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Leishmania braziliensis LbrM.35.7010   2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Leishmania donovani LdBPK_366960.1   2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Leishmania infantum LinJ.36.6960   2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Leishmania major LmjF.36.6650   2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Leishmania mexicana LmxM.36.6650   2,3-bisphosphoglycerate-independent phosphoglycerate mutase,2,3-bisphosphoglycerate-independentphosphoglyce ra temutase
Loa Loa (eye worm) LOAG_08132   independent phosphoglycerate mutase isoform 2
Oryza sativa 4332728   Os03g0330200
Oryza sativa 4327493   Os01g0817700
Oryza sativa 4339133   Os05g0482700
Trypanosoma brucei gambiense Tbg972.10.9710   2,3-bisphosphoglycerate-independent phosphoglycerate mutase, putative
Trypanosoma brucei Tb927.10.7930   2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Trypanosoma congolense TcIL3000_10_6810   2,3-bisphosphoglycerate-independent phosphoglycerate mutase
Trypanosoma cruzi TcCLB.506247.330   2,3-bisphosphoglycerate-independent phosphoglycerate mutase, putative
Trichomonas vaginalis TVAG_188600   2,3-bisphosphoglycerate-independent phosphoglycerate mutase, putative
Wolbachia endosymbiont of Brugia malayi Wbm0403   phosphoglyceromutase

Essentiality

LmjF.36.6650 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb927.10.7930 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb927.10.7930 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb927.10.7930 Trypanosoma brucei significant loss of fitness in procyclic forms alsford
Tb927.10.7930 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b3612 Escherichia coli non-essential goodall
CELE_F57B10.3 Caenorhabditis elegans embryonic lethal wormbase
CELE_F57B10.3 Caenorhabditis elegans larval lethal wormbase
CELE_F57B10.3 Caenorhabditis elegans slow growth wormbase
CELE_F57B10.3 Caenorhabditis elegans sterile wormbase
Show/Hide essentiality data references
  • 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.
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • 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
  • 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
  • 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.
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • 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

Compound Source Reference
ChEMBL23 References
ChEMBL23 References
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ChEMBL23 References
ChEMBL23 References
ChEMBL23 References
ChEMBL23 References
ChEMBL23 References
ChEMBL23 References
ChEMBL23 References
ChEMBL23 References
ChEMBL23 References
ChEMBL23 References
ChEMBL23 References
ChEMBL23 References

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
0.0104 0.3787 1
0.0099 0.384 1
0.0097 0.2738 0.72
0.0097 0.3679 1
0.0104 0.3787 1
0.0104 0.3787 1
0.0098 0.3787 1
0.0104 0.3787 1
0.011 0.358 0.5386
0.0099 0.3581 1
0.0104 0.3787 1
0.011 0.358 0.5386
0.0104 0.3787 1
0.0104 0.3787 1
0.0097 0.2738 0.72
0.0098 0.3679 1

Assayability

Assay information

  • Assay for Phosphoglycerate Mutase (5.4.2.1 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.
  • ChEMBL
  • PUBCHEM_BIOASSAY: qHTS Validation Assay to Find Inhibitors of Phosphoglycerate Mutase. (Class of assay: confirmatory) [Related pubchem assays (depositor defined):AID504639]
  • 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.36.6650 purified protein BRENDA A protein with this EC number or name or sequence has been purified from Leishmania mexicana ( 1 )

Bibliographic References

2 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.36.6650 (Leishmania major), 2,3-bisphosphoglycerate-independent phosphoglycerate mutase
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