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New page: left|200px<br /><applet load="1x3n" size="450" color="white" frame="true" align="right" spinBox="true" caption="1x3n, resolution 2.30Å" /> '''Crystal structure of...
 
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[[Image:1x3n.gif|left|200px]]<br /><applet load="1x3n" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1x3n, resolution 2.30&Aring;" />
'''Crystal structure of AMPPNP bound Propionate kinase (TdcD) from Salmonella typhimurium'''<br />


==Overview==
==Crystal structure of AMPPNP bound Propionate kinase (TdcD) from Salmonella typhimurium==
Recently, it has been shown that l-threonine can be catabolized, non-oxidatively to propionate via 2-ketobutyrate. Propionate kinase (TdcD;, EC 2.7.2.-) catalyses the last step of this metabolic process by enabling, the conversion of propionyl phosphate and ADP to propionate and ATP. To, provide insights into the substrate-binding pocket and catalytic mechanism, of TdcD, the crystal structures of the enzyme from Salmonella typhimurium, in complex with ADP and AMPPNP have been determined to resolutions of 2.2A, and 2.3A, respectively, by molecular replacement using Methanosarcina, thermophila acetate kinase (MAK; EC 2.7.2.1). Propionate kinase, like, acetate kinase, contains a fold with the topology, betabetabetaalphabetaalphabetaalpha, identical with that of glycerol, kinase, hexokinase, heat shock cognaten 70 (Hsc70) and actin, the, superfamily of phosphotransferases. The structure consists of two domains, with the active site contained in a cleft at the domain interface., Examination of the active site pocket revealed a plausible structural, rationale for the greater specificity of the enzyme towards propionate, than acetate. This was further confirmed by kinetic studies with the, purified enzyme, which showed about ten times lower K(m) for propionate, (2.3 mM) than for acetate (26.9 mM). Comparison of TdcD complex structures, with those of acetate and sugar kinase/Hsc70/actin obtained with different, ligands has permitted the identification of catalytically essential, residues involved in substrate binding and catalysis, and points to both, structural and mechanistic similarities. In the well-characterized members, of this superfamily, ATP phosphoryl transfer or hydrolysis is coupled to a, large conformational change in which the two domains close around the, active site cleft. The significant amino acid sequence similarity between, TdcD and MAK has facilitated study of domain movement, which indicates, that the conformation assumed by the two domains in the nucleotide-bound, structure of TdcD may represent an intermediate point in the pathway of, domain closure.
<StructureSection load='1x3n' size='340' side='right'caption='[[1x3n]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1x3n]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1X3N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X3N FirstGlance]. <br>
1X3N is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium] with EDO and ANP as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1X3N OCA].  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1x3n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x3n OCA], [https://pdbe.org/1x3n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x3n RCSB], [https://www.ebi.ac.uk/pdbsum/1x3n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x3n ProSAT]</span></td></tr>
Crystal structures of ADP and AMPPNP-bound propionate kinase (TdcD) from Salmonella typhimurium: comparison with members of acetate and sugar kinase/heat shock cognate 70/actin superfamily., Simanshu DK, Savithri HS, Murthy MR, J Mol Biol. 2005 Sep 30;352(4):876-92. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16139298 16139298]
</table>
[[Category: Salmonella typhimurium]]
== Function ==
[[Category: Single protein]]
[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]
[[Category: Murthy, M.R.]]
== Evolutionary Conservation ==
[[Category: Savithri, H.S.]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Simanshu, D.K.]]
Check<jmol>
[[Category: ANP]]
  <jmolCheckbox>
[[Category: EDO]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/x3/1x3n_consurf.spt"</scriptWhenChecked>
[[Category: amppnp]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: l-threonine metabolism]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: propionate kinase]]
  </jmolCheckbox>
[[Category: propionate metabolism]]
</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=1x3n ConSurf].
[[Category: tdcd]]
<div style="clear:both"></div>
 
__TOC__
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 05:49:24 2007''
</StructureSection>
[[Category: Large Structures]]
[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
[[Category: Murthy MR]]
[[Category: Savithri HS]]
[[Category: Simanshu DK]]

Latest revision as of 13:36, 13 March 2024

Crystal structure of AMPPNP bound Propionate kinase (TdcD) from Salmonella typhimurium

1x3n, resolution 2.30Å

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