Detailed view for PF3D7_0216000

Basic information

TDR Targets ID: 3423
Plasmodium falciparum, DEAD/DEAH box helicase, putative
Source Database / ID:  PlasmoDB   |   GeneDB   |   MPMP

pI: 7.2756 | Length (AA): 1997 | MW (Da): 237127 | Paralog Number: 0

Signal peptide: N | GPI Anchor: N | 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

PF00176   SNF2 family N-terminal domain
PF00271   Helicase conserved C-terminal domain

Gene Ontology

Mouse over links to read term descriptions.
GO:0016514   SWI/SNF complex  
GO:0016252   nonspecific RNA polymerase II transcription factor activity  
GO:0004386   helicase activity  
GO:0003678   DNA helicase activity  
GO:0003677   DNA binding  
GO:0003676   nucleic acid binding  
GO:0005524   ATP binding  
GO:0006338   chromatin remodeling  

Metabolic Pathways

This gene is not mapped to any metabolic pathway in KEGG.

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
866 1356 1z6a (A) 7 900 26.00 0 1 0.56 -0.37
880 1262 1z6a (A) 440 801 33.00 0 1 0.62 -0.85
4 165 3k29 (A) 11 162 19.00 0.63 0.08 0.265122 -0.74
90 422 4hte (A) 263 592 24.00 0.074 0.98 0.34485 0.02
94 270 3na7 (A) 3 188 29.00 0.025 0.07 0.428733 -1.71
114 215 4wik (A) 489 596 25.00 0.38 0 0.571177 -3.28
471 719 4wat (A) 185 491 28.00 0.94 0.39 0.190787 0.45
665 1537 3mwy (W) 190 921 38.00 0 1 0.395256 1.44
885 1577 1z3i (X) 148 734 24.00 0 1 0.223021 1.06
906 1069 3dmq (A) 174 342 27.00 0.29 0.83 0.339223 0.28
1269 1375 3ult (A) 5 115 36.00 0.14 0.24 0.33568 -1.06
1770 1956 4uos (A) 2 183 20.00 0.0026 0.14 0.40764 -1.48
1 366 4hte (A) 261 592 25.00 0.55 0.69 0.297623 0.65
2 185 3na7 (A) 11 183 23.00 0.039 0.1 0.289384 -0.45
26 241 4tql (A) 16 222 26.00 0.0066 0.31 0.239294 -0.13
67 250 4uos (A) 2 183 18.00 0.39 0.02 0.411684 -1.86
162 471 4dkj (A) 58 312 34.00 0.75 0.3 0.0763799 1.48
605 1453 3mwy (W) 190 921 38.00 0 1 0.456842 1.29
826 1493 1z3i (X) 149 734 22.00 0 1 0.355125 0.72
846 1009 3dmq (A) 174 342 27.00 0.28 0.83 0.34314 0.28
1694 1874 4uos (A) 1 183 19.00 0.016 0.12 0.334817 -1.2

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

Upregulation Percent Ranking Stage Dataset
Upper 80-100% percentile gametocyte, Female Gametocyte, Male Gametocyte. PlasmoDB Lasonder E
Upregulation Percent Ranking Stage Dataset
Upper 60-80% percentile Sporozoite. Zanghi G
Upregulation Percent Ranking Stage Dataset
Mid 40-60% percentile late schizont, Oocyst. PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 20-40% percentile intra-erythrocytic - 0 hs, intra-erythrocytic - 8 hs, intra-erythrocytic - 16 hs, intra-erythrocytic - 40 hs, early schizont, Ring. Otto TD PlasmoDB Zanghi G
Upregulation Percent Ranking Stage Dataset
Lower 0-20% percentile intra-erythrocytic - 24 hs, intra-erythrocytic - 32 hs, intra-erythrocytic - 48 hs. Otto TD
Show/Hide expression data references
  • Zanghi G A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
  • PlasmoDB Data on upregulation of P. falciparum genes in different life cycle stages, combined from several microarray experiments available in PlasmoDB
  • Otto TD New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
  • Lasonder E Integrated transcriptomic and proteomic analyses of P. falciparum gametocytes. Molecular insight into sex-specific processes and translational repression.

Orthologs

Ortholog group members (OG5_127595)

Species Accession Gene Product
Arabidopsis thaliana AT3G06010   SNF2/Brahma-type chromatin-remodeling protein CHR12
Arabidopsis thaliana AT5G19310   homeotic protein regulator
Arabidopsis thaliana AT2G28290   chromatin structure-remodeling complex protein SYD
Brugia malayi Bm1_51990   BRM protein
Candida albicans CaO19.239   DNA helicase
Candida albicans CaO19.7869   DNA helicase
Candida albicans CaO19.9102   transcriptional regulator
Candida albicans CaO19.1526   transcriptional regulator
Caenorhabditis elegans CELE_F01G4.1   Protein SWSN-4
Caenorhabditis elegans CELE_C52B9.8   Protein C52B9.8
Cryptosporidium parvum cgd2_3700   SWI/SNF related putative transcriptional regulator ATpase
Cryptosporidium parvum cgd8_2300   brahma like protein with a HSA domain, SNF2 like helicase and a bromo domain
Dictyostelium discoideum DDB_G0271052   CHR group protein
Dictyostelium discoideum DDB_G0285205   CHR group protein
Drosophila melanogaster Dmel_CG5942   brahma
Echinococcus granulosus EgrG_000636800   global transcription activator snf2l2
Echinococcus multilocularis EmuJ_000636800   global transcription activator snf2l2
Homo sapiens ENSG00000080503   SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2
Homo sapiens ENSG00000127616   SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4
Loa Loa (eye worm) LOAG_01607   BRM protein
Loa Loa (eye worm) LOAG_06505   BRM protein
Mus musculus ENSMUSG00000024921   SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2
Mus musculus ENSMUSG00000032187   SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4
Neospora caninum NCLIV_067550   hypothetical protein
Neospora caninum NCLIV_009850   SNF2 family N-terminal domain-containing protein (EC 2.7.11.1), related
Oryza sativa 9271208   Os06g0255200
Oryza sativa 4337784   Os05g0144300
Plasmodium berghei PBANKA_0312700   DEAD/DEAH helicase, putative
Plasmodium falciparum PF3D7_0216000   DEAD/DEAH box helicase, putative
Plasmodium knowlesi PKNH_0404900   DEAD/DEAH helicase, putative
Plasmodium vivax PVX_002740   DEAD/DEAH helicase, putative
Plasmodium yoelii PY01120   Arabidopsis thaliana BRAHMA ortholog-related
Saccharomyces cerevisiae YOR290C   Snf2p
Saccharomyces cerevisiae YIL126W   RSC chromatin remodeling complex ATPase subunit STH1
Schistosoma japonicum Sjp_0132880   Homeotic gene regulator, putative
Schistosoma japonicum Sjp_0102960   ko:K01529 SMARCA2, SNF2L2; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 [EC
Schistosoma mansoni Smp_158050   helicase
Schmidtea mediterranea mk4.006072.02  
Schmidtea mediterranea mk4.001874.03   ATP-dependent helicase brm
Schmidtea mediterranea mk4.001874.02  
Schmidtea mediterranea mk4.001874.01  
Schmidtea mediterranea mk4.006072.01  
Schmidtea mediterranea mk4.006072.00   ATP-dependent helicase brm
Toxoplasma gondii TGME49_278440   SWI2/SNF2 Brahma-like putative
Toxoplasma gondii TGME49_320300   SWI2/SNF2 Brahma-like putative
Trichomonas vaginalis TVAG_441050   lymphoid specific helicase, putative

Essentiality

PF3D7_0216000 has one or more orthologs with essentiality data
Gene/Ortholog Organism Phenotype Source Study
CELE_F01G4.1 Caenorhabditis elegans embryonic lethal wormbase
CELE_F01G4.1 Caenorhabditis elegans slow growth wormbase
CELE_F01G4.1 Caenorhabditis elegans sterile wormbase
YIL126W Saccharomyces cerevisiae inviable yeastgenome
PBANKA_0312700 Plasmodium berghei Dispensable plasmo
TGME49_320300 Toxoplasma gondii Probably essential sidik
TGME49_278440 Toxoplasma gondii Probably essential sidik
Show/Hide essentiality data references
  • yeastgenome Systematic deletion of yeast genes Saccharomyces Genome Database
  • neb C. elegans RNAi phenotypes Data obtained from Wormbase WS150, curated by K. Chaudary and T. Carlow, New England Biolabs
  • gerdes Experimental determination and system-level analysis of essential genes in E. coli MG1655 Gerdes et al., J Bacteriol. 2003 185:5673-84
  • 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.
  • shigen Profiling of E. coli Chromosome (PEC) National Institute of Genetics, Japan
  • 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.
  • 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
  • nmpdr Genome-scale essentiality datasets from published studies (M. tuberculosis) National Microbial Pathogen Data Resource
  • 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.
  • alsford High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome Genome Res 2011, 21:915-924
  • blattner Systematic mutagenesis of the E. coli (MG1655) genome J Bacteriol 2004, 186:4921-4930

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 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 Compounds References
Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 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

No literature references available for this target.

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 PF3D7_0216000 (Plasmodium falciparum), DEAD/DEAH box helicase, putative
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