7l29: Difference between revisions

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<StructureSection load='7l29' size='340' side='right'caption='[[7l29]], [[Resolution|resolution]] 2.08&Aring;' scene=''>
<StructureSection load='7l29' size='340' side='right'caption='[[7l29]], [[Resolution|resolution]] 2.08&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[7l29]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7L29 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L29 FirstGlance]. <br>
<table><tr><td colspan='2'>[[7l29]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7L29 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7L29 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.08&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PDE3A ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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=7l29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l29 OCA], [https://pdbe.org/7l29 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l29 RCSB], [https://www.ebi.ac.uk/pdbsum/7l29 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l29 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=7l29 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7l29 OCA], [https://pdbe.org/7l29 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7l29 RCSB], [https://www.ebi.ac.uk/pdbsum/7l29 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7l29 ProSAT]</span></td></tr>
</table>
</table>
== Disease ==
== Disease ==
[[https://www.uniprot.org/uniprot/PDE3A_HUMAN PDE3A_HUMAN]] Brachydactyly-arterial hypertension syndrome. The disease is caused by variants affecting the gene represented in this entry.  
[https://www.uniprot.org/uniprot/PDE3A_HUMAN PDE3A_HUMAN] Brachydactyly-arterial hypertension syndrome. The disease is caused by variants affecting the gene represented in this entry.
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/PDE3A_HUMAN PDE3A_HUMAN]] Cyclic nucleotide phosphodiesterase with a dual-specificity for the second messengers cAMP and cGMP, which are key regulators of many important physiological processes.[UniProtKB:Q9Z0X4]  
[https://www.uniprot.org/uniprot/PDE3A_HUMAN PDE3A_HUMAN] Cyclic nucleotide phosphodiesterase with a dual-specificity for the second messengers cAMP and cGMP, which are key regulators of many important physiological processes.[UniProtKB:Q9Z0X4]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
DNMDP and related compounds, or velcrins, induce complex formation between the phosphodiesterase PDE3A and the SLFN12 protein, leading to a cytotoxic response in cancer cells that express elevated levels of both proteins. The mechanisms by which velcrins induce complex formation, and how the PDE3A-SLFN12 complex causes cancer cell death, are not fully understood. Here, we show that PDE3A and SLFN12 form a heterotetramer stabilized by binding of DNMDP. Interactions between the C-terminal alpha helix of SLFN12 and residues near the active site of PDE3A are required for complex formation, and are further stabilized by interactions between SLFN12 and DNMDP. Moreover, we demonstrate that SLFN12 is an RNase, that PDE3A binding increases SLFN12 RNase activity, and that SLFN12 RNase activity is required for DNMDP response. This new mechanistic understanding will facilitate development of velcrin compounds into new cancer therapies.


Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase.,Garvie CW, Wu X, Papanastasiou M, Lee S, Fuller J, Schnitzler GR, Horner SW, Baker A, Zhang T, Mullahoo JP, Westlake L, Hoyt SH, Toetzl M, Ranaghan MJ, de Waal L, McGaunn J, Kaplan B, Piccioni F, Yang X, Lange M, Tersteegen A, Raymond D, Lewis TA, Carr SA, Cherniack AD, Lemke CT, Meyerson M, Greulich H Nat Commun. 2021 Jul 16;12(1):4375. doi: 10.1038/s41467-021-24495-w. PMID:34272366<ref>PMID:34272366</ref>
==See Also==
 
*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7l29" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]
[[Category: Homo sapiens]]
[[Category: Human]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Garvie, C]]
[[Category: Garvie C]]
[[Category: Horner, S W]]
[[Category: Horner SW]]
[[Category: Hydrolase]]

Latest revision as of 17:58, 6 March 2024

Crystal structure of the catalytic domain of human PDE3A bound to AMPCrystal structure of the catalytic domain of human PDE3A bound to AMP

Structural highlights

7l29 is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.08Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

PDE3A_HUMAN Brachydactyly-arterial hypertension syndrome. The disease is caused by variants affecting the gene represented in this entry.

Function

PDE3A_HUMAN Cyclic nucleotide phosphodiesterase with a dual-specificity for the second messengers cAMP and cGMP, which are key regulators of many important physiological processes.[UniProtKB:Q9Z0X4]

See Also

7l29, resolution 2.08Å

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