2pvz: Difference between revisions

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{{Seed}}
[[Image:2pvz.png|left|200px]]


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==Crystal structure of methylaconitate isomerase PrpF from Shewanella oneidensis==
The line below this paragraph, containing "STRUCTURE_2pvz", creates the "Structure Box" on the page.
<StructureSection load='2pvz' size='340' side='right'caption='[[2pvz]], [[Resolution|resolution]] 1.97&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2pvz]] 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=2PVZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PVZ FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.97&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
{{STRUCTURE_2pvz|  PDB=2pvz  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pvz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pvz OCA], [https://pdbe.org/2pvz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pvz RCSB], [https://www.ebi.ac.uk/pdbsum/2pvz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pvz ProSAT]</span></td></tr>
</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/pv/2pvz_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2pvz ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


===Crystal structure of methylaconitate isomerase PrpF from Shewanella oneidensis===
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:17567742<ref>PMID:17567742</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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(as it appears on PubMed at http://www.pubmed.gov), where 17567742 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_17567742}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2PVZ is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PVZ OCA].
 
==Reference==
<ref group="xtra">PMID:17567742</ref><references group="xtra"/>
[[Category: Shewanella oneidensis]]
[[Category: Shewanella oneidensis]]
[[Category: Garvey, G S.]]
[[Category: Garvey GS]]
[[Category: Rayment, I R.]]
[[Category: Rayment IR]]
[[Category: Aconitate binding]]
[[Category: Diaminopimelate epimerase like]]
[[Category: Propionate catabolism]]
[[Category: Unknown function]]
 
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Retrieved from "https://proteopedia.org/2pvz"