This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3v93

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:34, 1 March 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='3v93' size='340' side='right'caption='[[3v93]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='3v93' size='340' side='right'caption='[[3v93]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3v93]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Trycr Trycr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V93 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V93 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3v93]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_cruzi Trypanosoma cruzi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V93 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V93 FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+
</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&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3v94|3v94]]</div></td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PDEC, Trypanosoma cruzi ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5693 TRYCR])</td></tr>
+
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.17 3.1.4.17] </span></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=3v93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v93 OCA], [https://pdbe.org/3v93 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v93 RCSB], [https://www.ebi.ac.uk/pdbsum/3v93 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v93 ProSAT]</span></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=3v93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v93 OCA], [https://pdbe.org/3v93 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v93 RCSB], [https://www.ebi.ac.uk/pdbsum/3v93 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v93 ProSAT]</span></td></tr>
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/Q53I60_TRYCR Q53I60_TRYCR]
-
Trypanosoma cruzi phosphodiesterase C (TcrPDEC) is a potential new drug target for the treatment of Chagas disease but has not been well studied. This study reports the enzymatic properties of various kinetoplastid PDECs and the crystal structures of the unliganded TcrPDEC1 catalytic domain and its complex with an inhibitor. Mutations of PDEC during the course of evolution led to inactivation of PDEC in Trypanosoma brucei/Trypanosoma evansi/Trypanosoma congolense, whereas the enzyme is active in all other kinetoplastids. The TcrPDEC1 catalytic domain hydrolyzes both cAMP and cGMP with a K(m) of 23.8 mum and a k(cat) of 31 s(-1) for cAMP and a K(m) of 99.1 mum and a k(cat) of 17 s(-1) for cGMP, thus confirming its dual specificity. The crystal structures show that the N-terminal fragment wraps around the TcrPDEC catalytic domain and may thus regulate its enzymatic activity via direct interactions with the active site residues. A PDE5 selective inhibitor that has an IC(50) of 230 nm for TcrPDEC1 binds to TcrPDEC1 in an orientation opposite to that of sildenafil. This observation, together with the screen of the inhibitory potency of human PDE inhibitors against TcrPDEC, implies that the scaffold of some human PDE inhibitors might be used as the starting model for design of parasite PDE inhibitors. The structural study also identified a unique parasite pocket that neighbors the active site and may thus be valuable for the design of parasite-specific inhibitors.
+
-
 
+
-
Biological and structural characterization of Trypanosoma cruzi phosphodiesterase C and Implications for design of parasite selective inhibitors.,Wang H, Kunz S, Chen G, Seebeck T, Wan Y, Robinson H, Martinelli S, Ke H J Biol Chem. 2012 Apr 6;287(15):11788-97. Epub 2012 Feb 21. PMID:22356915<ref>PMID:22356915</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 3v93" style="background-color:#fffaf0;"></div>
+
==See Also==
==See Also==
*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
-
== References ==
 
-
<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Trycr]]
+
[[Category: Trypanosoma cruzi]]
-
[[Category: Chen, G]]
+
[[Category: Chen G]]
-
[[Category: Ke, H]]
+
[[Category: Ke H]]
-
[[Category: Kunz, S]]
+
[[Category: Kunz S]]
-
[[Category: Martinelli, S]]
+
[[Category: Martinelli S]]
-
[[Category: Robinson, H]]
+
[[Category: Robinson H]]
-
[[Category: Seebeck, T]]
+
[[Category: Seebeck T]]
-
[[Category: Wan, Y]]
+
[[Category: Wan Y]]
-
[[Category: Wang, H]]
+
[[Category: Wang H]]
-
[[Category: Hydrolase]]
+
-
[[Category: Parasite]]
+
-
[[Category: Phosphodiesterase]]
+

Current revision

unliganded structure of TcrPDEC1 catalytic domain

PDB ID 3v93

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3v93"
Personal tools