Structural highlights
Function
[OPR1_ARATH] Specifically cleaves olefinic bonds in alpha,beta-unsaturated carbonyls and may be involved in detoxification or modification of these reactive compounds. May be involved in the biosynthesis or metabolism of oxylipin signaling molecules. In vitro, reduces 9R,13R-12-oxophyodienoic acid (9R,13R-OPDA) to 9R,13R-OPC-8:0, but only poorly 9S,13S-OPDA, the natural precursor of jasmonic acid. Can detoxify the explosive 2,4,6-trinitrotoluene (TNT) in vitro and in vivo by catalyzing its nitroreduction to form hydroxylamino-dinitrotoluene (HADNT).[1]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.
Ensemble refinement of protein crystal structures: validation and application.,Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr Structure. 2007 Sep;15(9):1040-52. PMID:17850744[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Beynon ER, Symons ZC, Jackson RG, Lorenz A, Rylott EL, Bruce NC. The role of oxophytodienoate reductases in the detoxification of the explosive 2,4,6-trinitrotoluene by Arabidopsis. Plant Physiol. 2009 Sep;151(1):253-61. doi: 10.1104/pp.109.141598. Epub 2009 Jul , 15. PMID:19605548 doi:http://dx.doi.org/10.1104/pp.109.141598
- ↑ Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr. Ensemble refinement of protein crystal structures: validation and application. Structure. 2007 Sep;15(9):1040-52. PMID:17850744 doi:http://dx.doi.org/10.1016/j.str.2007.06.019
