3ib8: Difference between revisions

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-{{Seed}}
-[[Image:3ib8.jpg|left|200px]]
-<!--
+==Crystal structure of full length Rv0805 in complex with 5'-AMP==
-The line below this paragraph, containing "STRUCTURE_3ib8", creates the "Structure Box" on the page.
+<StructureSection load='3ib8' size='340' side='right'caption='[[3ib8]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3ib8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IB8 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]] 1.8&#8491;</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=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
-{{STRUCTURE_3ib8|  PDB=3ib8  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ib8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ib8 OCA], [https://pdbe.org/3ib8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ib8 RCSB], [https://www.ebi.ac.uk/pdbsum/3ib8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ib8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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>
+== 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/ib/3ib8_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=3ib8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Mycobacterium tuberculosis utilizes many mechanisms to establish itself within the macrophage, and bacterially derived cAMP is important in modulating the host cellular response. Although the genome of M. tuberculosis is endowed with a number of mammalian-like adenylyl cyclases, only a single cAMP phosphodiesterase has been identified that can decrease levels of cAMP produced by the bacterium. We present the crystal structure of the full-length and sole cAMP phosphodiesterase, Rv0805, found in M. tuberculosis, whose orthologs are present only in the genomes of slow growing and pathogenic mycobacteria. The dimeric core catalytic domain of Rv0805 adopts a metallophosphoesterase-fold, and the C-terminal region builds the active site and contributes to multiple substrate utilization. Localization of Rv0805 to the cell wall is dependent on its C terminus, and expression of either wild type or mutationally inactivated Rv0805 in M. smegmatis alters cell permeability to hydrophobic cytotoxic compounds. Rv0805 may therefore play a key role in the pathogenicity of mycobacteria, not only by hydrolyzing bacterial cAMP, but also by moonlighting as a protein that can alter cell wall functioning.
-===Crystal structure of full length Rv0805 in complex with 5'-AMP===
+A mycobacterial cyclic AMP phosphodiesterase that moonlights as a modifier of cell wall permeability.,Podobnik M, Tyagi R, Matange N, Dermol U, Gupta AK, Mattoo R, Seshadri K, Visweswariah SS J Biol Chem. 2009 Nov 20;284(47):32846-57. Epub 2009 Sep 29. PMID:19801656<ref>PMID:19801656</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3ib8" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-IB8 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IB8 OCA].
+*[[Phosphodiesterase 3D structures|Phosphodiesterase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:17059828</ref><ref group="xtra">PMID:16313172</ref><references group="xtra"/>
+__TOC__
-[[Category: 3',5'-cyclic-nucleotide phosphodiesterase]]
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Mycobacterium tuberculosis]]
-[[Category: Dermol, U.]]
+[[Category: Dermol U]]
-[[Category: Podobnik, M.]]
+[[Category: Podobnik M]]
-[[Category: Alpha-beta fold]]
-[[Category: Hydrolase]]
-[[Category: Metallophosphoesterase]]
-[[Category: Swapped-dimer]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 30 09:29:56 2009''