4fwl

From Proteopedia

(Difference between revisions)

Revision as of 05:12, 5 August 2016

Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with Phosphate (PO4)

Structural highlights

4fwl is a 1 chain structure with sequence from Salty. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	2e1y, 1x3m, 1x3n, 2e1z, 2e20, 4fwk, 4fwm, 4fwn, 4fwo, 4fwp, 4fwq, 4fwr, 4fws
Gene:	oxd-2, STM3242, tdcD (SALTY)
Activity:	Propionate kinase, with EC number 2.7.2.15
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4fwl"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with Phosphate (PO4)==
 <StructureSection load='4fwl' size='340' side='right' caption='[[4fwl]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
@@ Line 7: / Line 8: @@
 <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='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>
-<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=4fwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fwl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fwl RCSB], [http://www.ebi.ac.uk/pdbsum/4fwl PDBsum]</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=4fwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fwl OCA], [http://pdbe.org/4fwl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fwl RCSB], [http://www.ebi.ac.uk/pdbsum/4fwl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fwl ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 19: / Line 20: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4fwl" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

4fwl

From Proteopedia

Revision as of 05:12, 5 August 2016

Crystal structure of Salmonella typhimurium propionate kinase (TdcD) in complex with Phosphate (PO4)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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