1s3n: Difference between revisions

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-[[Image:1s3n.gif|left|200px]]<br /><applet load="1s3n" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1s3n, resolution 2.50&Aring;" />
-'''Structural and Functional Characterization of a Novel Archaeal Phosphodiesterase'''<br />
-==Overview==
+==Structural and Functional Characterization of a Novel Archaeal Phosphodiesterase==
-Methanococcus jannaschii MJ0936 is a hypothetical protein of unknown, function with over 50 homologs found in many bacteria and Archaea. To help, define the molecular (biochemical and biophysical) function of MJ0936, we, determined its crystal structure at 2.4-A resolution and performed a, series of biochemical screens for catalytic activity. The overall fold of, this single domain protein consists of a four-layered structure formed by, two beta-sheets flanked by alpha-helices on both sides. The crystal, structure suggested its biochemical function to be a nuclease, phosphatase, or nucleotidase, with a requirement for some metal ions., Crystallization in the presence of Ni(2+) or Mn(2+) produced a protein, containing a binuclear metal center in the putative active site formed by, a cluster of conserved residues. Analysis of MJ0936 against a panel of, general enzymatic assays revealed catalytic activity toward, bis-p-nitrophenyl phosphate, an indicator substrate for phosphodiesterases, and nucleases. Significant activity was also found with two other, phosphodiesterase substrates, thymidine 5'-monophosphate p-nitrophenyl, ester and p-nitrophenylphosphorylcholine, but no activity was found for, cAMP or cGMP. Phosphodiesterase activity of MJ0936 had an absolute, requirement for divalent metal ions with Ni(2+) and Mn(2+) being most, effective. Thus, our structural and enzymatic studies have identified the, biochemical function of MJ0936 as that of a novel phosphodiesterase.
+<StructureSection load='1s3n' size='340' side='right'caption='[[1s3n]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1s3n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S3N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S3N FirstGlance]. <br>
-S3N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii] with MN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1S3N 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]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=1s3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s3n OCA], [https://pdbe.org/1s3n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s3n RCSB], [https://www.ebi.ac.uk/pdbsum/1s3n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s3n ProSAT], [https://www.topsan.org/Proteins/BSGC/1s3n TOPSAN]</span></td></tr>
-Structural and functional characterization of a novel phosphodiesterase from Methanococcus jannaschii., Chen S, Yakunin AF, Kuznetsova E, Busso D, Pufan R, Proudfoot M, Kim R, Kim SH, J Biol Chem. 2004 Jul 23;279(30):31854-62. Epub 2004 May 5. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15128743 15128743]
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/P936_METJA P936_METJA] Shows phosphodiesterase activity, hydrolyzing phosphodiesters bonds in the artificial chromogenic substrates bis-p-nitrophenyl phosphate (bis-pNPP), and less efficiently thymidine 5'-monophosphate p-nitrophenyl ester (pNP-TMP) and p-nitrophenylphosphorylcholine (pNPPC). No catalytic activity was found toward cAMP or cGMP, nucleotides or phospholipase substrates such as phosphatidylcholine. The physiological substrate is unknown.
+== 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/s3/1s3n_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=1s3n ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Methanocaldococcus jannaschii]]
-[[Category: Single protein]]
+[[Category: Busso D]]
-[[Category: BSGC, Berkeley.Structural.Genomics.Center.]]
+[[Category: Chen S]]
-[[Category: Busso, D.]]
+[[Category: Jancrick J]]
-[[Category: Chen, S.]]
+[[Category: Kim R]]
-[[Category: Jancrick, J.]]
+[[Category: Kim S-H]]
-[[Category: Kim, R.]]
+[[Category: Kuznetsova E]]
-[[Category: Kim, S.H.]]
+[[Category: Proudfoot M]]
-[[Category: Kuznetsova, E.]]
+[[Category: Yakunin AF]]
-[[Category: Proudfoot, M.]]
-[[Category: Yakunin, A.F.]]
-[[Category: MN]]
-[[Category: berkeley structural genomics center]]
-[[Category: bsgc structure funded by nih]]
-[[Category: di-metal-binding]]
-[[Category: phosphodiesterase/nuclease]]
-[[Category: protein structure initiative]]
-[[Category: psi]]
-[[Category: structural genomics]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:04:37 2007''