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New page: left|200px<br /><applet load="2pw0" size="350" color="white" frame="true" align="right" spinBox="true" caption="2pw0, resolution 1.57Å" /> '''crystal structure of...
 
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[[Image:2pw0.jpg|left|200px]]<br /><applet load="2pw0" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2pw0, resolution 1.57&Aring;" />
'''crystal structure of trans-aconitate bound to methylaconitate isomerase PrpF from Shewanella oneidensis'''<br />


==Overview==
==crystal structure of trans-aconitate bound to methylaconitate isomerase PrpF from Shewanella oneidensis==
In bacteria, the dehydration of 2-methylcitrate to yield 2-methylaconitate, in the 2-methylcitric acid cycle is catalyzed by a cofactor-less (PrpD), enzyme or by an aconitase-like (AcnD) enzyme. Bacteria that use AcnD also, require the function of the PrpF protein, whose function was previously, unknown. To gain insights into the function of PrpF, the three-dimensional, crystal structure of the PrpF protein from the bacterium Shewanella, oneidensis was solved at 2.0 A resolution. The protein fold of PrpF is, strikingly similar to those of the non-PLP-dependent diaminopimelate, epimerase from Haemophilus influenzae, a putative proline racemase from, Brucella melitensis, and to a recently deposited structure of a, hypothetical protein from Pseudomonas aeruginosa. Results from in vitro, studies show that PrpF isomerizes trans-aconitate to cis-aconitate. It is, proposed that PrpF catalysis of the cis-trans isomerization proceeds, through a base-catalyzed proton abstraction coupled with a rotation about, C2-C3 bond of 2-methylaconitate, and that residue Lys73 is critical for, PrpF function. The newly identified function of PrpF as a, non-PLP-dependent isomerase, together with the fact that PrpD-containing, bacteria do not require PrpF, suggest that the isomer of 2-methylaconitate, that serves as a substrate of aconitase must have the same stereochemistry, as that synthesized by PrpD. From this, it follows that the, 2-methylaconitate isomer generated by AcnD is not a substrate of, aconitase, and that PrpF is required to generate the correct isomer. As a, consequence, the isomerase activity of PrpF may now be viewed as an, integral part of the 2-methylcitric acid cycle.
<StructureSection load='2pw0' size='340' side='right'caption='[[2pw0]], [[Resolution|resolution]] 1.57&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[2pw0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PW0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PW0 FirstGlance]. <br>
2PW0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis] with <scene name='pdbligand=EDO:'>EDO</scene> and <scene name='pdbligand=TRC:'>TRC</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PW0 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]] 1.57&#8491;</td></tr>
 
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=TRC:TRICARBALLYLIC+ACID'>TRC</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=2pw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pw0 OCA], [https://pdbe.org/2pw0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pw0 RCSB], [https://www.ebi.ac.uk/pdbsum/2pw0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pw0 ProSAT]</span></td></tr>
The three-dimensional crystal structure of the PrpF protein of Shewanella oneidensis complexed with trans-aconitate: insights into its biological function., Garvey GS, Rocco CJ, Escalante-Semerena JC, Rayment I, Protein Sci. 2007 Jul;16(7):1274-84. Epub 2007 Jun 13. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17567742 17567742]
</table>
== Function ==
[https://www.uniprot.org/uniprot/PRPF_SHEON PRPF_SHEON] Involved in the catabolism of short chain fatty acids (SCFA) via the 2-methylcitrate cycle II (propionate degradation route). PrpF catalyzes the cis-trans isomerization of 2-methyl-aconitate through a base-catalyzed proton abstraction coupled with a rotation about C2-C3 bond of 2-methyl-aconitate.<ref>PMID:14702315</ref> <ref>PMID:17567742</ref>
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pw/2pw0_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=2pw0 ConSurf].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Shewanella oneidensis]]
[[Category: Shewanella oneidensis]]
[[Category: Single protein]]
[[Category: Garvey GS]]
[[Category: Garvey, G.S.]]
[[Category: Rayment IR]]
[[Category: Rayment, I.R.]]
[[Category: EDO]]
[[Category: TRC]]
[[Category: aconitate binding]]
[[Category: diaminopimelate epimerase like]]
[[Category: propionate catabolism]]
[[Category: unknown function]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 12:33:43 2008''

Latest revision as of 09:12, 21 February 2024

crystal structure of trans-aconitate bound to methylaconitate isomerase PrpF from Shewanella oneidensis

2pw0, resolution 1.57Å

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