3f9q: Difference between revisions

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{{Seed}}
[[Image:3f9q.jpg|left|200px]]


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==Re-refinement of uncomplexed plasmepsin II from Plasmodium falciparum.==
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<StructureSection load='3f9q' size='340' side='right'caption='[[3f9q]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3f9q]] is a 1 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=3F9Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F9Q 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]] 1.9&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3f9q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f9q OCA], [https://pdbe.org/3f9q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f9q RCSB], [https://www.ebi.ac.uk/pdbsum/3f9q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f9q ProSAT]</span></td></tr>
{{STRUCTURE_3f9q|  PDB=3f9q  |  SCENE=  }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/PLM2_PLAFX PLM2_PLAFX] During the asexual blood stage, participates in initial cleavage of native host hemoglobin (Hb) resulting in Hb denaturation (PubMed:11782538, PubMed:15574427, PubMed:8844673). May cleave preferentially denatured hemoglobin that has been cleaved by PMI (PubMed:8844673). Digestion of host Hb is an essential step which provides the parasite with amino acids for protein synthesis, and regulates osmolarity (Probable).<ref>PMID:11782538</ref> <ref>PMID:15574427</ref> <ref>PMID:8844673</ref>
== 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/f9/3f9q_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3f9q ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The carboxylate atoms of the two catalytic aspartic acid residues in aspartic proteases are nearly coplanar and in the uncomplexed form share an in-plane nucleophilic water molecule that is central to the mechanism of these enzymes. This note reports that while reviewing the electron-density maps derived from the deposited data for uncomplexed plasmepsin II from Plasmodium falciparum [Asojo et al. (2003), J. Mol. Biol. 327, 173-181; PDB code 1lf4], it was discovered that the aspartic acid residues in this structure should in fact be distinctly noncoplanar. The crystallographic model from the deposited coordinates has been re-refined against the 1.9 A resolution published diffraction data to an R(cryst) of 21.2% and an R(free) of 22.2%. The catalytic water molecule is present, but the plane of the carboxylate group of Asp214 is rotated by 66 degrees from its original position.


===Re-refinement of uncomplexed plasmepsin II from Plasmodium falciparum.===
Crystallographic evidence for noncoplanar catalytic aspartic acids in plasmepsin II resides in the Protein Data Bank.,Robbins AH, Dunn BM, Agbandje-McKenna M, McKenna R Acta Crystallogr D Biol Crystallogr. 2009 Mar;65(Pt 3):294-6. Epub 2009, Feb 20. PMID:19237752<ref>PMID:19237752</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3f9q" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_19237752}}, adds the Publication Abstract to the page
*[[Plasmepsin|Plasmepsin]]
(as it appears on PubMed at http://www.pubmed.gov), where 19237752 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_19237752}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
3F9Q is a 1 chain 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=3F9Q OCA].
 
==Reference==
<ref group="xtra">PMID:19237752</ref><ref group="xtra">PMID:12614616</ref><references group="xtra"/>
[[Category: Plasmepsin II]]
[[Category: Plasmodium falciparum]]
[[Category: Plasmodium falciparum]]
[[Category: Mckenna, R.]]
[[Category: Mckenna R]]
[[Category: Robbins, A H.]]
[[Category: Robbins AH]]
[[Category: Aspartyl protease]]
[[Category: Glycoprotein]]
[[Category: Hydrolase]]
[[Category: Protease]]
[[Category: Vacuole]]
[[Category: Zymogen]]
 
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Retrieved from "https://proteopedia.org/3f9q"