2pvz: Difference between revisions
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'''Crystal structure of methylaconitate isomerase PrpF from Shewanella oneidensis''' | {{Structure | ||
|PDB= 2pvz |SIZE=350|CAPTION= <scene name='initialview01'>2pvz</scene>, resolution 1.97Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene> | |||
|ACTIVITY= | |||
|GENE= PrpF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70863 Shewanella oneidensis]) | |||
}} | |||
'''Crystal structure of methylaconitate isomerase PrpF from Shewanella oneidensis''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2PVZ is a [ | 2PVZ is a [[Single protein]] structure of sequence 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== | ==Reference== | ||
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:// | 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://www.ncbi.nlm.nih.gov/pubmed/17567742 17567742] | ||
[[Category: Shewanella oneidensis]] | [[Category: Shewanella oneidensis]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
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[[Category: unknown function]] | [[Category: unknown function]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:18:06 2008'' | ||
Revision as of 16:18, 20 March 2008
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| 2pvz, resolution 1.97Å | |||||||||||||
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| Ligands: | CA and EDO | ||||||||||||
| Gene: | PrpF (Shewanella oneidensis) | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
Crystal structure of methylaconitate isomerase PrpF from Shewanella oneidensis
Overview
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.
About this Structure
2PVZ is a Single protein structure of sequence from Shewanella oneidensis. Full crystallographic information is available from OCA.
Reference
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
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