2f6i: Difference between revisions

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[[Image:2f6i.gif|left|200px]]


<!--
==Crystal structure of the ClpP protease catalytic domain from Plasmodium falciparum==
The line below this paragraph, containing "STRUCTURE_2f6i", creates the "Structure Box" on the page.
<StructureSection load='2f6i' size='340' side='right'caption='[[2f6i]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2f6i]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F6I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F6I FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.45&#8491;</td></tr>
-->
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f6i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f6i OCA], [https://pdbe.org/2f6i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f6i RCSB], [https://www.ebi.ac.uk/pdbsum/2f6i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f6i ProSAT]</span></td></tr>
{{STRUCTURE_2f6i|  PDB=2f6i  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/O97252_PLAF7 O97252_PLAF7]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f6/2f6i_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2f6i ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The Clp chaperones and proteases play an important role in protein homeostasis in the cell. They are highly conserved across prokaryotes and found also in the mitochondria of eukaryotes and the chloroplasts of plants. They function mainly in the disaggregation, unfolding and degradation of native as well as misfolded proteins. Here, we provide a comprehensive analysis of the Clp chaperones and proteases in the human malaria parasite Plasmodium falciparum. The parasite contains four Clp ATPases, which we term PfClpB1, PfClpB2, PfClpC and PfClpM. One PfClpP, the proteolytic subunit, and one PfClpR, which is an inactive version of the protease, were also identified. Expression of all Clp chaperones and proteases was confirmed in blood-stage parasites. The proteins were localized to the apicoplast, a non-photosynthetic organelle that accommodates several important metabolic pathways in P. falciparum, with the exception of PfClpB2 (also known as Hsp101), which was found in the parasitophorous vacuole. Both PfClpP and PfClpR form mostly homoheptameric rings as observed by size-exclusion chromatography, analytical ultracentrifugation and electron microscopy. The X-ray structure of PfClpP showed the protein as a compacted tetradecamer similar to that observed for Streptococcus pneumoniae and Mycobacterium tuberculosis ClpPs. Our data suggest the presence of a ClpCRP complex in the apicoplast of P. falciparum.


'''Crystal structure of the ClpP protease catalytic domain from Plasmodium falciparum'''
The Clp chaperones and proteases of the human malaria parasite Plasmodium falciparum.,El Bakkouri M, Pow A, Mulichak A, Cheung KL, Artz JD, Amani M, Fell S, de Koning-Ward TF, Goodman CD, McFadden GI, Ortega J, Hui R, Houry WA J Mol Biol. 2010 Dec 3;404(3):456-77. Epub 2010 Sep 29. PMID:20887733<ref>PMID:20887733</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2f6i" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
Parasites from the protozoan phylum Apicomplexa are responsible for diseases, such as malaria, toxoplasmosis and cryptosporidiosis, all of which have significantly higher rates of mortality and morbidity in economically underdeveloped regions of the world. Advances in vaccine development and drug discovery are urgently needed to control these diseases and can be facilitated by production of purified recombinant proteins from Apicomplexan genomes and determination of their 3D structures. To date, both heterologous expression and crystallization of Apicomplexan proteins have seen only limited success. In an effort to explore the effectiveness of producing and crystallizing proteins on a genome-scale using a standardized methodology, over 400 distinct Plasmodium falciparum target genes were chosen representing different cellular classes, along with select orthologues from four other Plasmodium species as well as Cryptosporidium parvum and Toxoplasma gondii. From a total of 1008 genes from the seven genomes, 304 (30.2%) produced purified soluble proteins and 97 (9.6%) crystallized, culminating in 36 crystal structures. These results demonstrate that, contrary to previous findings, a standardized platform using Escherichia coli can be effective for genome-scale production and crystallography of Apicomplexan proteins. Predictably, orthologous proteins from different Apicomplexan genomes behaved differently in expression, purification and crystallization, although the overall success rates of Plasmodium orthologues do not differ significantly. Their differences were effectively exploited to elevate the overall productivity to levels comparable to the most successful ongoing structural genomics projects: 229 of the 468 target genes produced purified soluble protein from one or more organisms, with 80 and 32 of the purified targets, respectively, leading to crystals and ultimately structures from one or more orthologues.
*[[Clp protease 3D structures|Clp protease 3D structures]]
 
== References ==
==About this Structure==
<references/>
2F6I is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F6I OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms., Vedadi M, Lew J, Artz J, Amani M, Zhao Y, Dong A, Wasney GA, Gao M, Hills T, Brokx S, Qiu W, Sharma S, Diassiti A, Alam Z, Melone M, Mulichak A, Wernimont A, Bray J, Loppnau P, Plotnikova O, Newberry K, Sundararajan E, Houston S, Walker J, Tempel W, Bochkarev A, Kozieradzki I, Edwards A, Arrowsmith C, Roos D, Kain K, Hui R, Mol Biochem Parasitol. 2007 Jan;151(1):100-10. Epub 2006 Nov 13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17125854 17125854]
[[Category: Endopeptidase Clp]]
[[Category: Plasmodium falciparum]]
[[Category: Plasmodium falciparum]]
[[Category: Single protein]]
[[Category: Amani M]]
[[Category: Amani, M.]]
[[Category: Arrowsmith C]]
[[Category: Arrowsmith, C.]]
[[Category: Bray J]]
[[Category: Bray, J.]]
[[Category: Edwards A]]
[[Category: Edwards, A.]]
[[Category: Finerty P]]
[[Category: Finerty, P.]]
[[Category: Hui R]]
[[Category: Hui, R.]]
[[Category: Loppnau P]]
[[Category: Loppnau, P.]]
[[Category: Mulichak A]]
[[Category: Mulichak, A.]]
[[Category: Plotnikova O]]
[[Category: Plotnikova, O.]]
[[Category: Sundstrom M]]
[[Category: SGC, Structural Genomics Consortium.]]
[[Category: Vedadi M]]
[[Category: Sundstrom, M.]]
[[Category: Wasney G]]
[[Category: Vedadi, M.]]
[[Category: Weigelt J]]
[[Category: Wasney, G.]]
[[Category: Weigelt, J.]]
[[Category: Clp protease]]
[[Category: Sgc]]
[[Category: Structural genomic]]
[[Category: Structural genomics consortium]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 03:31:15 2008''

Latest revision as of 10:44, 23 August 2023

Crystal structure of the ClpP protease catalytic domain from Plasmodium falciparumCrystal structure of the ClpP protease catalytic domain from Plasmodium falciparum

Structural highlights

2f6i is a 7 chain structure with sequence from Plasmodium falciparum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.45Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

O97252_PLAF7

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The Clp chaperones and proteases play an important role in protein homeostasis in the cell. They are highly conserved across prokaryotes and found also in the mitochondria of eukaryotes and the chloroplasts of plants. They function mainly in the disaggregation, unfolding and degradation of native as well as misfolded proteins. Here, we provide a comprehensive analysis of the Clp chaperones and proteases in the human malaria parasite Plasmodium falciparum. The parasite contains four Clp ATPases, which we term PfClpB1, PfClpB2, PfClpC and PfClpM. One PfClpP, the proteolytic subunit, and one PfClpR, which is an inactive version of the protease, were also identified. Expression of all Clp chaperones and proteases was confirmed in blood-stage parasites. The proteins were localized to the apicoplast, a non-photosynthetic organelle that accommodates several important metabolic pathways in P. falciparum, with the exception of PfClpB2 (also known as Hsp101), which was found in the parasitophorous vacuole. Both PfClpP and PfClpR form mostly homoheptameric rings as observed by size-exclusion chromatography, analytical ultracentrifugation and electron microscopy. The X-ray structure of PfClpP showed the protein as a compacted tetradecamer similar to that observed for Streptococcus pneumoniae and Mycobacterium tuberculosis ClpPs. Our data suggest the presence of a ClpCRP complex in the apicoplast of P. falciparum.

The Clp chaperones and proteases of the human malaria parasite Plasmodium falciparum.,El Bakkouri M, Pow A, Mulichak A, Cheung KL, Artz JD, Amani M, Fell S, de Koning-Ward TF, Goodman CD, McFadden GI, Ortega J, Hui R, Houry WA J Mol Biol. 2010 Dec 3;404(3):456-77. Epub 2010 Sep 29. PMID:20887733[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ El Bakkouri M, Pow A, Mulichak A, Cheung KL, Artz JD, Amani M, Fell S, de Koning-Ward TF, Goodman CD, McFadden GI, Ortega J, Hui R, Houry WA. The Clp chaperones and proteases of the human malaria parasite Plasmodium falciparum. J Mol Biol. 2010 Dec 3;404(3):456-77. Epub 2010 Sep 29. PMID:20887733 doi:10.1016/j.jmb.2010.09.051

2f6i, resolution 2.45Å

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