1k20

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Current revision (07:43, 7 February 2024) (edit) (undo)
 
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<StructureSection load='1k20' size='340' side='right'caption='[[1k20]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
<StructureSection load='1k20' size='340' side='right'caption='[[1k20]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[1k20]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_10558 Atcc 10558]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K20 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K20 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[1k20]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_gordonii Streptococcus gordonii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K20 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K20 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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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]] 1.5&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1k23|1k23]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] </span></td></tr>
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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=1k20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k20 OCA], [https://pdbe.org/1k20 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k20 RCSB], [https://www.ebi.ac.uk/pdbsum/1k20 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k20 ProSAT]</span></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=1k20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k20 OCA], [https://pdbe.org/1k20 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k20 RCSB], [https://www.ebi.ac.uk/pdbsum/1k20 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k20 ProSAT]</span></td></tr>
</table>
</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PPAC_STRGC PPAC_STRGC]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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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=1k20 ConSurf].
</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=1k20 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
 
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== Publication Abstract from PubMed ==
 
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Recently, a new class of soluble inorganic pyrophosphatase (type-C PPase) has been described that is not homologous in amino acid sequence or kinetic properties to the well-studied PPases (types A and B) found in many organisms from bacteria to humans and thought to be essential to the cell. Structural studies of the type-C PPases from Streptococcus gordonii and Bacillus subtilis reveal a homodimeric structure, with each polypeptide folding into two domains joined by a flexible hinge. The active site, formed at the interface between the N and C-terminal domains, binds two manganese ions approximately 3.6 A apart in a conformation resembling binuclear metal centres found in other hydrolytic enzymes. An activated water molecule bridging the two metal ions is likely poised for nucleophilic attack of the substrate. Importantly, the S. gordonii and B. subtilis enzymes have crystallised in strikingly different conformations. In both subunits of the S. gordonii crystal structure (1.5 A resolution) the C-terminal domain is positioned such that the active site is occluded, with a sulphate ion bound in the active site. In contrast, in the B. subtilis structure (3.0 A resolution) the C-terminal domain is rotated by about 90 degrees, leaving the active site wide open and accessible for substrate binding.
 
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The "open" and "closed" structures of the type-C inorganic pyrophosphatases from Bacillus subtilis and Streptococcus gordonii.,Ahn S, Milner AJ, Futterer K, Konopka M, Ilias M, Young TW, White SA J Mol Biol. 2001 Nov 2;313(4):797-811. PMID:11697905<ref>PMID:11697905</ref>
 
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
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</div>
 
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<div class="pdbe-citations 1k20" style="background-color:#fffaf0;"></div>
 
==See Also==
==See Also==
*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]]
*[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Atcc 10558]]
 
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[[Category: Inorganic diphosphatase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Ahn, S]]
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[[Category: Streptococcus gordonii]]
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[[Category: Futterer, K]]
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[[Category: Ahn S]]
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[[Category: Ilias, M]]
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[[Category: Futterer K]]
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[[Category: Konopka, M]]
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[[Category: Ilias M]]
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[[Category: Milner, A J]]
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[[Category: Konopka M]]
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[[Category: White, S A]]
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[[Category: Milner AJ]]
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[[Category: Young, T W]]
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[[Category: White SA]]
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[[Category: Binuclear metal centre]]
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[[Category: Young TW]]
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[[Category: Family ii ppase]]
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[[Category: Hydrolase]]
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[[Category: Manganese]]
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Current revision

Inorganic Pyrophosphatase (family II) from Streptococcus gordonii at 1.5 A resolution

PDB ID 1k20

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