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| | ==Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with GMP== | | ==Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with GMP== |
| - | <StructureSection load='4fwo' size='340' side='right' caption='[[4fwo]], [[Resolution|resolution]] 2.90Å' scene=''> | + | <StructureSection load='4fwo' size='340' side='right'caption='[[4fwo]], [[Resolution|resolution]] 2.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4fwo]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Salty Salty]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FWO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FWO FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4fwo]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FWO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FWO FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 2.9Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2e1y|2e1y]], [[1x3m|1x3m]], [[1x3n|1x3n]], [[2e1z|2e1z]], [[2e20|2e20]], [[4fwk|4fwk]], [[4fwl|4fwl]], [[4fwm|4fwm]], [[4fwn|4fwn]], [[4fwp|4fwp]], [[4fwq|4fwq]], [[4fwr|4fwr]], [[4fws|4fws]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">oxd-2, STM3242, tdcD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</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=4fwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fwo OCA], [https://pdbe.org/4fwo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fwo RCSB], [https://www.ebi.ac.uk/pdbsum/4fwo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fwo 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/Propionate_kinase Propionate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.2.15 2.7.2.15] </span></td></tr>
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| - | <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=4fwo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fwo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fwo RCSB], [http://www.ebi.ac.uk/pdbsum/4fwo PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/TDCD_SALTY TDCD_SALTY]] Catalyzes the conversion of propionyl phosphate and ADP to propionate and ATP. It can also use acetyl phosphate as phosphate group acceptor.[HAMAP-Rule:MF_01881] | + | [https://www.uniprot.org/uniprot/TDCD_SALTY TDCD_SALTY] Catalyzes the conversion of propionyl phosphate and ADP to propionate and ATP. It can also use acetyl phosphate as phosphate group acceptor.[HAMAP-Rule:MF_01881] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4fwo" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Propionate kinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Salty]] | + | [[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]] |
| - | [[Category: Chittori, S]] | + | [[Category: Chittori S]] |
| - | [[Category: Murthy, M R.N]] | + | [[Category: Murthy MRN]] |
| - | [[Category: Savithri, H S]] | + | [[Category: Savithri HS]] |
| - | [[Category: Gmp]]
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| - | [[Category: Kinase]]
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| - | [[Category: Short-chain fatty acid]]
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| - | [[Category: Tdcd]]
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| - | [[Category: Transferase]]
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| Structural highlights
Function
TDCD_SALTY Catalyzes the conversion of propionyl phosphate and ADP to propionate and ATP. It can also use acetyl phosphate as phosphate group acceptor.[HAMAP-Rule:MF_01881]
Publication Abstract from PubMed
Short-chain fatty acids (SCFAs) play a major role in carbon cycle and can be utilized as a source of carbon and energy by bacteria. Salmonella typhimurium propionate kinase (StTdcD) catalyzes reversible transfer of the gamma-phosphate of ATP to propionate during l-threonine degradation to propionate. Kinetic analysis revealed that StTdcD possesses broad ligand specificity and could be activated by various SCFAs (propionate>acetate approximately butyrate), nucleotides (ATP approximately GTP>CTP approximately TTP; dATP>dGTP>dCTP) and metal ions (Mg(2+) approximately Mn(2+)>Co(2+)). Inhibition of StTdcD by tricarboxylic acid (TCA) cycle intermediates such as citrate, succinate, alpha-ketoglutarate and malate suggests that the enzyme could be under plausible feedback regulation. Crystal structures of StTdcD bound to PO4 (phosphate), AMP, ATP, Ap4 (adenosine tetraphosphate), GMP, GDP, GTP, CMP and CTP revealed that binding of nucleotide mainly involves hydrophobic interactions with the base moiety and could account for the broad biochemical specificity observed between the enzyme and nucleotides. Modeling and site-directed mutagenesis studies suggest Ala88 to be an important residue involved in determining the rate of catalysis with SCFA substrates. Molecular dynamics simulations on monomeric and dimeric forms of StTdcD revealed plausible open and closed states, and also suggested role for dimerization in stabilizing segment 235-290 involved in interfacial interactions and ligand binding. Observation of an ethylene glycol molecule bound sufficiently close to the gamma-phosphate in StTdcD complexes with triphosphate nucleotides supports direct in-line phosphoryl transfer.
Mechanistic features of Salmonella typhimurium propionate kinase (TdcD): insights from kinetic and crystallographic studies.,Chittori S, Simanshu DK, Banerjee S, Murthy AM, Mathivanan S, Savithri HS, Murthy MR Biochim Biophys Acta. 2013 Oct;1834(10):2036-44. doi:, 10.1016/j.bbapap.2013.05.020. Epub 2013 Jun 5. PMID:23747922[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Chittori S, Simanshu DK, Banerjee S, Murthy AM, Mathivanan S, Savithri HS, Murthy MR. Mechanistic features of Salmonella typhimurium propionate kinase (TdcD): insights from kinetic and crystallographic studies. Biochim Biophys Acta. 2013 Oct;1834(10):2036-44. doi:, 10.1016/j.bbapap.2013.05.020. Epub 2013 Jun 5. PMID:23747922 doi:http://dx.doi.org/10.1016/j.bbapap.2013.05.020
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