2hyo: Difference between revisions

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-[[Image:2hyo.gif|left|200px]]<br /><applet load="2hyo" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="2hyo, resolution 2.250&Aring;" />
-'''Crystal structure of Rv0805 N97A mutant'''<br />
-==Overview==
+==Crystal structure of Rv0805 N97A mutant==
-Cyclic nucleotide monophosphate (cNMP) hydrolysis in bacteria and eukaryotes is brought about by distinct cNMP phosphodiesterases (PDEs). Since these enzymes differ in amino acid sequence and properties, they have evolved by convergent evolution. Cyclic NMP PDEs cleave cNMPs to NMPs, and the Rv0805 gene product is, to date, the only identifiable cNMP PDE in the genome of Mycobacterium tuberculosis. We have shown that Rv0805 is a cAMP/cGMP dual specificity PDE, and is unrelated in amino acid sequence to the mammalian cNMP PDEs. Rv0805 is a dimeric, Fe(3+)-Mn(2+) binuclear PDE, and mutational analysis demonstrated that the active site metals are co-ordinated by conserved aspartate, histidine and asparagine residues. We report here the structure of the catalytic core of Rv0805, which is distantly related to the calcineurin-like phosphatases. The crystal structure of the Rv0805 dimer shows that the active site metals contribute to dimerization and thus play an additional structural role apart from their involvement in catalysis. We also present the crystal structures of the Asn97Ala mutant protein that lacks one of the Mn(2+) co-ordinating residues as well as the Asp66Ala mutant that has a compromised cAMP hydrolytic activity, providing a structural basis for the catalytic properties of these mutant proteins. A molecule of phosphate is bound in a bidentate manner at the active site of the Rv0805 wild-type protein, and cacodylate occupies a similar position in the crystal structure of the Asp66Ala mutant protein. A unique substrate binding pocket in Rv0805 was identified by computational docking studies, and the role of the His140 residue in interacting with cAMP was validated through mutational analysis. This report on the first structure of a bacterial cNMP PDE thus significantly extends our molecular understanding of cAMP hydrolysis in class III PDEs.
+<StructureSection load='2hyo' size='340' side='right'caption='[[2hyo]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[2hyo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HYO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HYO FirstGlance]. <br>
-HYO is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis] with <scene name='pdbligand=FE:'>FE</scene> and <scene name='pdbligand=MN:'>MN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/3',5'-cyclic-nucleotide_phosphodiesterase 3',5'-cyclic-nucleotide phosphodiesterase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.4.17 3.1.4.17] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HYO OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2hyo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hyo OCA], [https://pdbe.org/2hyo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hyo RCSB], [https://www.ebi.ac.uk/pdbsum/2hyo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hyo ProSAT]</span></td></tr>
-Structural and biochemical analysis of the Rv0805 cyclic nucleotide phosphodiesterase from Mycobacterium tuberculosis., Shenoy AR, Capuder M, Draskovic P, Lamba D, Visweswariah SS, Podobnik M, J Mol Biol. 2007 Jan 5;365(1):211-25. Epub 2006 Oct 6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17059828 17059828]
+</table>
-[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]
+== Function ==
-[[Category: Mycobacterium tuberculosis]]
+[https://www.uniprot.org/uniprot/CNPD3_MYCTU CNPD3_MYCTU] Cyclic nucleotide phosphodiesterase with a dual-specificity for the second messengers cAMP and cGMP (PubMed:16313172, PubMed:18757371). Can use 2',3'-cAMP, 2',3'-cGMP, 3',5'-cAMP, 3',5'-cGMP and 3',5'-cUMP (PubMed:16313172, PubMed:18757371, PubMed:19801656). Hydrolysis of 2',3'-cAMP produces a mixture of 3'-AMP (major product) and 2'-AMP (minor product) (PubMed:18757371). In vitro, is 150-fold more active in hydrolyzing 2',3'-cAMP than 3',5'-cAMP (PubMed:18757371). Can also hydrolyze the model substrates p-nitrophenyl phosphate (pNPP), bis-(p-nitrophenyl phosphate) (bis(pNPP)) and p-nitrophenyl phenylphosphonate (pNPPP) (PubMed:16313172, PubMed:18757371, PubMed:19801656). Plays an important regulatory role in modulating the intracellular concentration of cAMP, thereby influencing cAMP-dependent processes (PubMed:16313172). May play a role in pathogenicity, not only by hydrolyzing cAMP, but also by altering properties of the cell wall (PubMed:19801656).<ref>PMID:16313172</ref> <ref>PMID:18757371</ref> <ref>PMID:19801656</ref>   Overexpression elicits a transcriptional response that is independent of the phosphodiesterase activity. It does not alter the levels of cAMP-CRP regulated genes, even though cAMP levels are reduced in cells.<ref>PMID:23835087</ref>
-[[Category: Single protein]]
+== Evolutionary Conservation ==
-[[Category: Capuder, M.]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: Draskovic, P.]]
+Check<jmol>
-[[Category: Lamba, D.]]
+  <jmolCheckbox>
-[[Category: Podobnik, M.]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hy/2hyo_consurf.spt"</scriptWhenChecked>
-[[Category: Shenoy, A R.]]
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-[[Category: Visweswariah, S S.]]
+    <text>to colour the structure by Evolutionary Conservation</text>
-[[Category: FE]]
+  </jmolCheckbox>
-[[Category: MN]]
+</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=2hyo ConSurf].
-[[Category: bi-nuclear active site]]
+<div style="clear:both"></div>
-[[Category: camp]]
+== References ==
-[[Category: metallophosphoesterase]]
+<references/>
-[[Category: phosphodiesterase]]
+__TOC__
+</StructureSection>
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:47:13 2008''
+[[Category: Large Structures]]
+[[Category: Mycobacterium tuberculosis H37Rv]]
+[[Category: Capuder M]]
+[[Category: Draskovic P]]
+[[Category: Lamba D]]
+[[Category: Podobnik M]]
+[[Category: Shenoy AR]]
+[[Category: Visweswariah SS]]