1wpm

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[[Image:1wpm.jpg|left|200px]]
 
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{{Structure
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==Structure of Bacillus subtilis inorganic pyrophosphatase==
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|PDB= 1wpm |SIZE=350|CAPTION= <scene name='initialview01'>1wpm</scene>, resolution 2.05&Aring;
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<StructureSection load='1wpm' size='340' side='right'caption='[[1wpm]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=PG4:TETRAETHYLENE GLYCOL'>PG4</scene>
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<table><tr><td colspan='2'>[[1wpm]] 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=1WPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WPM FirstGlance]. <br>
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|ACTIVITY= [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]
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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]] 2.05&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1wpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wpm OCA], [https://pdbe.org/1wpm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wpm RCSB], [https://www.ebi.ac.uk/pdbsum/1wpm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wpm ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PPAC_BACSU PPAC_BACSU]
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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/wp/1wpm_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=1wpm ConSurf].
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<div style="clear:both"></div>
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'''Structure of Bacillus subtilis inorganic pyrophosphatase'''
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==See Also==
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*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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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.
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==About this Structure==
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1WPM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WPM OCA].
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==Reference==
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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://www.ncbi.nlm.nih.gov/pubmed/15533045 15533045]
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[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
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[[Category: Inorganic diphosphatase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Baykov AA]]
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[[Category: Baykov, A A.]]
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[[Category: Fabrichniy IP]]
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[[Category: Fabrichniy, I P.]]
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[[Category: Goldman A]]
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[[Category: Goldman, A.]]
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[[Category: Lahti R]]
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[[Category: Lahti, R.]]
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[[Category: Lehtio L]]
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[[Category: Lehtio, L.]]
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[[Category: Salminen A]]
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[[Category: Salminen, A.]]
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[[Category: PG4]]
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[[Category: SO4]]
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[[Category: inorganic pyrophosphatase]]
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[[Category: metal binding]]
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[[Category: ppase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:00:05 2008''
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Current revision

Structure of Bacillus subtilis inorganic pyrophosphatase

PDB ID 1wpm

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OCA

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