Detailed view for PF3D7_1033100

Basic information

TDR Targets ID: 1396
Plasmodium falciparum, S-adenosylmethionine decarboxylase/ornithine decarboxylase
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 6.3101 | Length (AA): 1434 | MW (Da): 168170 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | Predicted trans-membrane segments: 0

Druggability Group : DG3

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

PF00278   Pyridoxal-dependent decarboxylase, C-terminal sheet domain
PF01536   Adenosylmethionine decarboxylase
PF02784   Pyridoxal-dependent decarboxylase, pyridoxal binding domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0009445   putrescine metabolic process  
GO:0005575   cellular_component  
GO:0004586   ornithine decarboxylase activity  
GO:0004014   adenosylmethionine decarboxylase activity  
GO:0003824   catalytic activity  
GO:0008295   spermidine biosynthetic process  
GO:0006597   spermine biosynthetic process  
GO:0006596   polyamine biosynthetic process  

Structural information

Modbase 3D models:

There are 21 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
4 329 1jl0 (A) 6 308 20.00 0 1 0.06 0.27
5 181 1jl0 (A) 7 143 37.00 0.000009 0.91 0.22 -0.01
820 1260 1twi (A) 15 442 17.00 0 1 0.38 0.1
855 1050 1w8g (A) 7 205 13.00 0 0.75 0.14 -0.69
4 497 1jl0 (A) 6 306 26.00 0 0.99 -0.255109 2.03
5 181 1jl0 (A) 7 143 38.00 0.0000047 0.92 0.172231 0.72
118 740 3s5k (A) 60 687 18.00 0.000000057 0.99 0.459249 1.15
415 473 3ep6 (A) 223 281 41.00 0.1 0.98 0.424944 0.43
809 1432 2oo0 (A) 0 422 36.00 0 1 0.170546 1.89
821 1259 3n2b (A) 0 410 17.00 0.00000034 1 0.312537 0.48
855 1418 1f3t (A) 44 408 43.00 0 1 0.0871054 1.65
1183 1284 3ult (A) 9 113 28.00 0.58 0.38 0.33893 -1.11
415 473 3ep6 (A) 223 281 42.00 0.055 0.99 0.444979 0.34
590 730 3na7 (A) 27 166 14.00 0.33 0.01 0.267566 -0.46
796 1417 2oo0 (A) 0 422 35.00 0 1 0.203537 1.56
806 1258 3vab (A) 0 421 15.00 0 1 0.340439 0.7
823 1405 1f3t (A) 19 410 40.00 0 1 0.0980527 1.84
827 1170 4aib (B) 17 330 31.00 0 1 0.286724 0.88
829 1258 1twi (A) 37 446 16.00 0 1 0.34923 0.45
831 1216 2nva (A) 12 355 30.00 0.00000000051 1 0.493223 0.3
838 1259 3btn (A) 40 435 25.00 0.000000000055 1 0.469593 -0.01

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
  • 1M9V:
  • Resolution Method # Atoms # Residues Dep. Date Pub. Date Mod. Date

Expression

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 40 hs, intra-erythrocytic - 48 hs, gametocyte, merozoite, sporozoite, early ring, early schizont, early trophozoite, late ring, late schizont, late trophozoite, Oocyst, Ring, Sporozoite, Female Gametocyte. Otto TD PlasmoDB Zanghi G Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Male Gametocyte. Lasonder E
Show/Hide expression data references
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.

Orthologs

Ortholog group members (OG5_126750)

Species Accession Gene Product
Arabidopsis thaliana AT3G14390   diaminopimelate decarboxylase 1
Arabidopsis thaliana AT5G11880   diaminopimelate decarboxylase 2
Brugia malayi Bm1_56455   Pyridoxal-dependent decarboxylase, pyridoxal binding domain containing protein
Candida albicans CaO19.6032   Ornithine decarboxylase similar to S. cerevisiae SPE1 (YKL184W) involved in pantothenate and polyamine biosynthesis
Candida albicans CaO19.13453   Ornithine decarboxylase similar to S. cerevisiae SPE1 (YKL184W) involved in pantothenate and polyamine biosynthesis
Caenorhabditis elegans CELE_K11C4.4   Protein ODC-1
Dictyostelium discoideum DDB_G0281109   Orn/DAP/Arg decarboxylase 2 domain-containing protein
Dictyostelium discoideum DDB_G0269856   Orn/DAP/Arg decarboxylase 2 domain-containing protein
Drosophila melanogaster Dmel_CG8719   Ornithine decarboxylase 2
Drosophila melanogaster Dmel_CG8721   Ornithine decarboxylase 1
Escherichia coli b2838   diaminopimelate decarboxylase, PLP-binding
Entamoeba histolytica EHI_100430   ornithine decarboxylase, putative
Giardia lamblia GL50803_94582   Ornithine decarboxylase
Homo sapiens ENSG00000115758   ornithine decarboxylase 1
Leishmania braziliensis LbrM.12.0300   ornithine decarboxylase, putative
Leishmania donovani LdBPK_120105.1   ornithine decarboxylase, putative
Leishmania infantum LinJ.12.0100   ornithine decarboxylase, putative
Leishmania major LmjF.12.0280   ornithine decarboxylase, putative
Leishmania mexicana LmxM.12.0280   ornithine decarboxylase, putative
Loa Loa (eye worm) LOAG_07980   pyridoxal-dependent decarboxylase
Mycobacterium leprae ML1128   PROBABLE DIAMINOPIMELATE DECARBOXYLASE LYSA (DAP DECARBOXYLASE)
Mus musculus ENSMUSG00000023120   predicted gene 853
Mus musculus ENSMUSG00000011179   ornithine decarboxylase, structural 1
Mycobacterium tuberculosis Rv1293   Diaminopimelate decarboxylase LysA (DAP decarboxylase)
Mycobacterium ulcerans MUL_3971   diaminopimelate decarboxylase LysA
Neospora caninum NCLIV_067260   Diaminopimelate decarboxylase protein, related
Oryza sativa 4329234   Os02g0440000
Oryza sativa 4347746   Os09g0543400
Oryza sativa 4335010   Os04g0136500
Onchocerca volvulus OVOC1740  
Plasmodium berghei PBANKA_0516900   S-adenosylmethionine decarboxylase/ornithine decarboxylase, putative
Plasmodium falciparum PF3D7_1033100   S-adenosylmethionine decarboxylase/ornithine decarboxylase
Plasmodium knowlesi PKNH_0617900   S-adenosylmethionine decarboxylase/ornithine decarboxylase, putative
Plasmodium vivax PVX_111070   S-adenosylmethionine decarboxylase-ornithine decarboxylase, putative
Plasmodium yoelii PY04754   S-adenosylmethionine decarboxylase-ornithine decarboxylase-related
Saccharomyces cerevisiae YKL184W   ornithine decarboxylase SPE1
Schmidtea mediterranea mk4.013057.00  
Schmidtea mediterranea mk4.012821.00  
Schmidtea mediterranea mk4.008099.00  
Schmidtea mediterranea mk4.023368.00  
Schmidtea mediterranea mk4.025019.00  
Schmidtea mediterranea mk4.007677.03  
Schmidtea mediterranea mk4.001750.03   Ornithine decarboxylase-1
Schmidtea mediterranea mk4.000699.03  
Schmidtea mediterranea mk4.014212.00  
Schmidtea mediterranea mk4.005186.01  
Schmidtea mediterranea mk4.021206.00  
Schmidtea mediterranea mk4.016468.00  
Schmidtea mediterranea mk4.022984.00  
Schmidtea mediterranea mk4.008099.01  
Schmidtea mediterranea mk4.008445.00  
Schmidtea mediterranea mk4.000260.08  
Schmidtea mediterranea mk4.009657.00  
Schmidtea mediterranea mk4.003300.00  
Trypanosoma brucei gambiense Tbg972.11.15320   ornithine decarboxylase, putative
Trypanosoma brucei Tb927.11.13730   ornithine decarboxylase
Trypanosoma congolense TcIL3000_0_32090   ornithine decarboxylase
Trypanosoma congolense TcIL3000.11.14030   ornithine decarboxylase, putative
Toxoplasma gondii TGME49_278740   diaminopimelate decarboxylase
Trichomonas vaginalis TVAG_001640   pyridoxal-dependent decarboxylase, putative
Trichomonas vaginalis TVAG_258030   ornithine decarboxylase, putative
Trichomonas vaginalis TVAG_205840   ornithine decarboxylase, putative
Trichomonas vaginalis TVAG_351660   diaminopimelate decarboxylase, putative
Trichomonas vaginalis TVAG_257110   diaminopimelate decarboxylase, putative
Trichomonas vaginalis TVAG_372420   conserved hypothetical protein

Essentiality

PF3D7_1033100 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
Tb11.01.5300 Trypanosoma brucei significant loss of fitness in bloodstream forms (3 days) alsford
Tb11.01.5300 Trypanosoma brucei significant loss of fitness in bloodstream forms (6 days) alsford
Tb11.01.5300 Trypanosoma brucei no significant loss or gain of fitness in procyclic forms alsford
Tb11.01.5300 Trypanosoma brucei significant loss of fitness in differentiation of procyclic to bloodstream forms alsford
b2838 Escherichia coli non-essential goodall
PBANKA_0516900 Plasmodium berghei Essential plasmo
TGME49_278740 Toxoplasma gondii Probably non-essential sidik
Show/Hide essentiality data references
  • 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.
  • wormbase C. elegans RNAi experiments WormBase web site, http://www.wormbase.org, release WS170
  • 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
  • keio Systematic single-gene knock-out mutants of E. coli K12 The Keio Collection
  • 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.
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database

Phenotypes and Validation (curated)

Annotated phenotypes:

Affected Entity Phenotypic quality Occurs in Occurs at Evidence Observed in Drugs/Inhibitors
growth (GO:0040007) lethal (sensu genetics) (PATO:0000718) multi-cellular organism (CARO:0000012) bloodstream stage (PLO:0040) host (GO:0018995) Plasmodium berghei 59964  
Annotator: saralph@unimelb.edu.au. Comment: 012/Mar/09. References: 2463635
growth (GO:0040007) lethal (sensu genetics) (PATO:0000718) multi-cellular organism (CARO:0000012) bloodstream stage (PLO:0040) in vivo inhibition (TDR:00016) Plasmodium falciparum 59964  
Annotator: saralph@unimelb.edu.au. Comment: 012/Mar/09. References: 2463635
catalytic activity (GO:0003824) decreased (PATO:0000468) in vitro (MI:0492) inferred from specific protein inhibition (ECO:0000020) Plasmodium falciparum 59964  
Annotator: saralph@unimelb.edu.au. Comment: 012/Mar/09. References: 12557188

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): 0.8

Known modulators for this target

Compound Source Reference
Curated by TDRTargets References

Predicted associations

By orthology with druggable targets
Species Known druggable target Linked compounds Reference
Rattus norvegicus Ornithine decarboxylase Compounds References
Homo sapiens ornithine decarboxylase 1 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
0.0664 0.4162 1
0.022 0.4102 1
0.0172 0.304 0.8233
0.0137 1 0.5
0.0098 0.2644 0.7895
0.0147 1 1
0.0102 0.2646 1
0.0059 0.4269 1
0.0375 0.3352 1
0.0486 0.4828 1
0.0072 1 0.5
0.0371 0.3827 0.5
0.065 0.4802 1
0.0651 0.4651 0.5
0.0286 0.4515 0.5
0.0066 1 1
0.0205 1 1
0.007 0.3463 0.5
0.0543 0.4606 0.5
0.0139 0.3288 0.5
0.0248 0.2629 1
0.0103 0.3417 1
0.0371 0.2643 0.5245
0.0243 0.3361 1
0.0234 0.6627 1
0.0124 0.3742 1
0.0433 0.4588 0.5
0.0152 0.3064 1
0.0134 0.4217 1
0.0239 0.7899 1
0.0377 0.2667 0.5258
0.0195831 0.381312 1
0.0122 0.3144 1
0.0122 0.2673 1
0.0494 0.4582 0.5
0.0252 0.6408 1
0.0122 0.3743 1
0.0242 0.6684 1
0.0158 0.4468 1
0.0245 0.3375 1
0.0242 0.6684 1
0.00646428 1 0.5
0.0107 0.3813 0.786
0.0166 0.4529 1
0.012 0.2832 1
0.0059 0.4269 1
0.0384 0.2652 0.5255
0.0127 0.6172 0
0.0249 0.6563 1
0.012 0.4486 1
0.0379 0.4274 1
0.0058 0.3871 1
0.0072 0.7179 0.5
0.0392 0.475 1
0.0379 0.2676 0.3363
0.0128 0.8693 0.5
0.0165 0.2826 0
0.0627 0.4857 1
0.0246 0.8245 1
0.065 0.3932 1
0.0124 0.3742 1
0.0146 0.2911 1
0.0201 0.5072 1
0.0381 0.4717 1
0.0256 0.3373 0.5
0.0375 0.3352 1
0.0391 0.2633 0.3394
0.0155 1 0.5
0.0312 0.2972 0.5
0.0395 0.2654 0.3333
0.0386 0.2637 0.3392
0.0444 0.4792 1
0.0102 0.8506 1
0.0489 0.2896 1
0.0175 0.491 0.5
0.0103 0.3417 1
0.0098 0.2667 0.7895
0.0058 0.3312 1
0.0242 0.6684 1
0.0117 0.326 0.5
0.0139 0.6024 1
0.0106 0.4251 1
0.021 0.2799 1
0.0158 0.3099 1
0.0448 0.2508 0.3246
0.0387 0.263 0.3352
0.0063 0.4149 0.5
0.0105 0.314 0.5
0.0111 0.3199 0.5
0.0247 0.6468 1
0.0248 0.2629 1
0.0245 0.3112 1
0.0177 0.4839 1
0.0556 0.4734 1
0.0377 0.267 0.3348
0.0245 0.3112 1
0.0214 0.4789 0.5
0.0275 0.4503 1
0.0213 0.2849 1
0.0058 0.3145 1
0.0161 0.4267 1
0.0379 0.2662 0.5248
0.0258 0.2869 1
0.0379 0.4274 1
0.0114 0.3504 0.5
0.006 0.387 0.5
0.0243 0.3361 1
0.0172 0.304 0.8233
0.0059 0.4269 1
0.0264 0.3859 1
0.0246 0.323 1
0.0123 0.3784 1
0.024 0.7295 0.5
0.0135 1 0.5
0.0066 0.376 1
0.0243 0.6443 1
0.0244 0.7029 1
0.0067 0.4196 0.5
0.0139 1 0.5
0.0177 0.5524 1
0.0235 0.6445 1
0.0072 0.7179 0.5
0.0602 0.3703 1
0.0264 0.3211 0.3168
0.0367 0.4601 0.5
0.0665 0.43 1
0.0203 0.2864 0.314
0.0129 0.4371 1
0.0165 0.4763 0.5
0.0201 1 1
0.0259 0.7094 1
0.0144078 0.318171 1

Assayability

Assay information

  • Assay for L-Ornithine Decarboxylase (4.1.1.17 ) Sigma-Aldrich
  • Automatic link to known assays based on EC numbers.
  • BRENDA Assay
  • An enzyme with this EC number or name or sequence has been assayed in Plasmodium falciparum ( 3 )

Reagent availability

  • Reagent:
  • Target Type Source Notes
    PF3D7_1033100 purified protein BRENDA A protein with this EC number or name or sequence has been purified from Plasmodium falciparum ( 3 )

Bibliographic References

30 literature references were collected for this gene.

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Gene identifier PF3D7_1033100 (Plasmodium falciparum), S-adenosylmethionine decarboxylase/ornithine decarboxylase
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