1wpn: Difference between revisions

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-[[Image:1wpn.jpg|left|200px]]<br /><applet load="1wpn" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1wpn, resolution 1.30&Aring;" />
-'''Crystal structure of the N-terminal core of Bacillus subtilis inorganic pyrophosphatase'''<br />
-==Overview==
+==Crystal structure of the N-terminal core of Bacillus subtilis inorganic pyrophosphatase==
-Family II inorganic pyrophosphatases (PPases) constitute a new, evolutionary group of PPases, with a different fold and mechanism than the, common family I enzyme; they are related to the "DHH" family of, phosphoesterases. Biochemical studies have shown that Mn(2+) and Co(2+), preferentially activate family II PPases; Mg(2+) partially activates; and, Zn(2+) can either activate or inhibit (Zyryanov et al., Biochemistry, 43, 14395-14402, accompanying paper in this issue). The three solved family II, PPase structures did not explain the differences between the PPase, families nor the metal ion differences described above. We therefore, solved three new family II PPase structures: Bacillus subtilis PPase, (Bs-PPase) dimer core bound to Mn(2+) at 1.3 A resolution, and, at 2.05 A, resolution, metal-free Bs-PPase and Streptococcus gordonii (Sg-PPase), containing sulfate and Zn(2+). Comparison of the new and old structures of, various family II PPases demonstrates why the family II enzyme prefers, Mn(2+) or Co(2+), as an activator rather than Mg(2+). Both M1 and M2, undergo significant changes upon substrate binding, changing from, five-coordinate to octahedral geometry. Mn(2+) and Co(2+), which readily, adopt different coordination states and geometries, are thus favored., Combining our structures with biochemical data, we identified M2 as the, high-affinity metal site. Zn(2+) activates in the M1 site, where, octahedral geometry is not essential for catalysis, but inhibits in the M2, site, because it is unable to assume octahedral geometry but remains, trigonal bipyramidal. Finally, we propose that Lys205-Gln81-Gln80 form a, hydrophilic channel to speed product release from the active site.
+<StructureSection load='1wpn' size='340' side='right'caption='[[1wpn]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1wpn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WPN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WPN FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1wpn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpn OCA], [https://pdbe.org/1wpn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wpn RCSB], [https://www.ebi.ac.uk/pdbsum/1wpn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wpn ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PPAC_BACSU PPAC_BACSU]
+== 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/wp/1wpn_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=1wpn ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-WPN is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with MN and SO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1WPN OCA].
+*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-Structural studies of metal ions in family II pyrophosphatases: the requirement for a Janus ion., Fabrichniy IP, Lehtio L, Salminen A, Zyryanov AB, Baykov AA, Lahti R, Goldman A, Biochemistry. 2004 Nov 16;43(45):14403-11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15533045 15533045]
 [[Category: Bacillus subtilis]]
-[[Category: Inorganic diphosphatase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Baykov AA]]
-[[Category: Baykov, A.A.]]
+[[Category: Fabrichniy IP]]
-[[Category: Fabrichniy, I.P.]]
+[[Category: Goldman A]]
-[[Category: Goldman, A.]]
+[[Category: Lahti R]]
-[[Category: Lahti, R.]]
+[[Category: Lehtio L]]
-[[Category: Lehtio, L.]]
+[[Category: Salminen A]]
-[[Category: Salminen, A.]]
-[[Category: MN]]
-[[Category: SO4]]
-[[Category: inorganic pyrophosphatase]]
-[[Category: metal binding]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 05:35:13 2007''