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| | ==Crystal structure of inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with Mg ions== | | ==Crystal structure of inorganic pyrophosphatase from Mycobacterium tuberculosis in complex with Mg ions== |
| - | <StructureSection load='4z71' size='340' side='right' caption='[[4z71]], [[Resolution|resolution]] 1.85Å' scene=''> | + | <StructureSection load='4z71' size='340' side='right'caption='[[4z71]], [[Resolution|resolution]] 1.85Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4z71]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z71 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Z71 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4z71]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Z71 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Z71 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4z70|4z70]], [[4z72|4z72]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ppa, Rv3628, MTCY15C10.24 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=4z71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z71 OCA], [https://pdbe.org/4z71 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4z71 RCSB], [https://www.ebi.ac.uk/pdbsum/4z71 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4z71 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4z71 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4z71 OCA], [http://pdbe.org/4z71 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4z71 RCSB], [http://www.ebi.ac.uk/pdbsum/4z71 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4z71 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/IPYR_MYCTU IPYR_MYCTU] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 4z71" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 4z71" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Inorganic pyrophosphatase 3D structures|Inorganic pyrophosphatase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Inorganic diphosphatase]] | + | [[Category: Large Structures]] |
| - | [[Category: Myctu]] | + | [[Category: Mycobacterium tuberculosis H37Rv]] |
| - | [[Category: Biswas, T]] | + | [[Category: Biswas T]] |
| - | [[Category: Pratt, A C]] | + | [[Category: Pratt AC]] |
| - | [[Category: Tsodikov, O V]] | + | [[Category: Tsodikov OV]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Inorganic pyrophosphate]]
| + | |
| - | [[Category: Phosphatase]]
| + | |
| - | [[Category: Pyrophosphatase]]
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| Structural highlights
Function
IPYR_MYCTU
Publication Abstract from PubMed
Family I inorganic pyrophosphatases (PPiases) are ubiquitous enzymes that are critical for phosphate metabolism in all domains of life. The detailed catalytic mechanism of these enzymes, including the identity of the general base, is not fully understood. We determined a series of crystal structures of the PPiase from Mycobacterium tuberculosis (Mtb PPiase) bound to catalytic metals, inorganic pyrophosphate (PPi; the reaction substrate) and to one or two inorganic phosphate ions (Pi; the reaction product), ranging in resolution from 1.85 to 3.30A. These structures represent a set of major kinetic intermediates in the catalytic turnover pathway for this enzyme and suggest an order of association and dissociation of the divalent metals, the substrate and the two products during the catalytic turnover. The active site of Mtb PPiase exhibits significant structural differences from the well characterized Escherichia coli PPiase in the vicinity of the bound PPi substrate. Prompted by these differences, quantum mechanics/molecular mechanics (QM/MM) analysis yielded an atomic description of the hydrolysis step for Mtb PPiase and, unexpectedly, indicated that Asp89, rather than Asp54 that was proposed for E. coli PPiase, can abstract a proton from a water molecule to activate it for a nucleophilic attack on the PPi substrate. Mutagenesis studies of the key Asp residues of Mtb PPiase supported this mechanism. This combination of structural and computational analyses clarifies our understanding of the mechanism of family I PPiases and has potential utility for rational development of drugs targeting this enzyme.
Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis.,Pratt AC, Dewage SW, Pang AH, Biswas T, Barnard-Britson S, Cisneros GA, Tsodikov OV J Struct Biol. 2015 Aug 19. pii: S1047-8477(15)30048-4. doi:, 10.1016/j.jsb.2015.08.010. PMID:26296329[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Pratt AC, Dewage SW, Pang AH, Biswas T, Barnard-Britson S, Cisneros GA, Tsodikov OV. Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis. J Struct Biol. 2015 Aug 19. pii: S1047-8477(15)30048-4. doi:, 10.1016/j.jsb.2015.08.010. PMID:26296329 doi:http://dx.doi.org/10.1016/j.jsb.2015.08.010
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