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2hd1

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[[Image:2hd1.gif|left|200px]]
 
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{{Structure
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==Crystal structure of PDE9 in complex with IBMX==
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|PDB= 2hd1 |SIZE=350|CAPTION= <scene name='initialview01'>2hd1</scene>, resolution 2.23&Aring;
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<StructureSection load='2hd1' size='340' side='right'caption='[[2hd1]], [[Resolution|resolution]] 2.23&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=IBM:3-ISOBUTYL-1-METHYLXANTHINE'>IBM</scene>
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<table><tr><td colspan='2'>[[2hd1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1tbm 1tbm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HD1 FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.23&#8491;</td></tr>
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|GENE= PDE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IBM:3-ISOBUTYL-1-METHYLXANTHINE'>IBM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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}}
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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=2hd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hd1 OCA], [https://pdbe.org/2hd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hd1 RCSB], [https://www.ebi.ac.uk/pdbsum/2hd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hd1 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PDE9A_HUMAN PDE9A_HUMAN] Hydrolyzes the second messenger cGMP, which is a key regulator of many important physiological processes.<ref>PMID:18757755</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hd/2hd1_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2hd1 ConSurf].
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<div style="clear:both"></div>
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'''Crystal structure of PDE9 in complex with IBMX'''
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==See Also==
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*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
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== References ==
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==Overview==
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<references/>
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Cyclic nucleotide phosphodiesterases (PDEs) are enzymes controlling cellular concentrations of the second messengers cAMP and cGMP. The crystal structure of the catalytic domain of PDE9A2, a member of a PDE family specifically hydrolyzing cGMP, has been determined at 2.23-A resolution. The PDE9A2 catalytic domain closely resembles the cAMP-specific PDE4D2 but is significantly different from the cGMP-specific PDE5A1, implying that each individual PDE family has its own characteristic substrate recognition mechanism. The different conformations of the H and M loops between PDE9A2 and PDE5A1 imply their less critical roles in nucleotide recognition. The nonselective inhibitor 3-isobutyl-1-methylxanthine (IBMX) binds to a similar subpocket in the active sites of PDE4, PDE5, and PDE9 and has a common pattern of the binding. However, significantly different orientations and interactions of IBMXs are observed among the three PDE families and also between two monomers of the PDE9A2 dimer. The kinetic properties of the PDE9A2 catalytic domain similar to those of full-length PDE9A imply that the N-terminal regulatory domain does not significantly alter the catalytic activity and the IBMX inhibition.
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__TOC__
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</StructureSection>
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==About this Structure==
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2HD1 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry 1TBM. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HD1 OCA].
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==Reference==
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Crystal structure of phosphodiesterase 9 shows orientation variation of inhibitor 3-isobutyl-1-methylxanthine binding., Huai Q, Wang H, Zhang W, Colman RW, Robinson H, Ke H, Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9624-9. Epub 2004 Jun 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15210993 15210993]
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Colman, R W.]]
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[[Category: Colman RW]]
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[[Category: Huai, Q.]]
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[[Category: Huai Q]]
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[[Category: Ke, H.]]
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[[Category: Ke H]]
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[[Category: Robinson, H.]]
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[[Category: Robinson H]]
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[[Category: Wang, H.]]
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[[Category: Wang H]]
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[[Category: Zhang, W.]]
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[[Category: Zhang W]]
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[[Category: IBM]]
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[[Category: MG]]
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[[Category: ZN]]
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[[Category: cgmp]]
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[[Category: ibmx]]
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[[Category: pde9]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:15:33 2008''
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Current revision

Crystal structure of PDE9 in complex with IBMX

PDB ID 2hd1

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