2pvz
From Proteopedia
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|PDB= 2pvz |SIZE=350|CAPTION= <scene name='initialview01'>2pvz</scene>, resolution 1.97Å | |PDB= 2pvz |SIZE=350|CAPTION= <scene name='initialview01'>2pvz</scene>, resolution 1.97Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> | + | |LIGAND= <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> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= PrpF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70863 Shewanella oneidensis]) | |GENE= PrpF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70863 Shewanella oneidensis]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2pw0|2PW0]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pvz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pvz OCA], [http://www.ebi.ac.uk/pdbsum/2pvz PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pvz RCSB]</span> | ||
}} | }} | ||
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[[Category: Garvey, G S.]] | [[Category: Garvey, G S.]] | ||
[[Category: Rayment, I R.]] | [[Category: Rayment, I R.]] | ||
| - | [[Category: CA]] | ||
| - | [[Category: EDO]] | ||
[[Category: aconitate binding]] | [[Category: aconitate binding]] | ||
[[Category: diaminopimelate epimerase like]] | [[Category: diaminopimelate epimerase like]] | ||
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[[Category: unknown function]] | [[Category: unknown function]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:41:28 2008'' |
Revision as of 01:41, 31 March 2008
| |||||||
| , resolution 1.97Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Gene: | PrpF (Shewanella oneidensis) | ||||||
| Related: | 2PW0
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| 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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