2q3r

From Proteopedia

(Difference between revisions)

Revision as of 14:44, 25 December 2014

Ensemble refinement of the protein crystal structure of At1g76680 from Arabidopsis thaliana

Structural highlights

2q3r is a 1 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1vji
Gene:	OPR1, At1g76680, F28O16.5 (Arabidopsis thaliana)
Activity:	12-oxophytodienoate reductase, with EC number 1.3.1.42
Resources:	FirstGlance, OCA, RCSB, PDBsum

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.

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2q3r"

@@ Line 9: / Line 9: @@
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q3r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3r OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q3r RCSB], [http://www.ebi.ac.uk/pdbsum/2q3r PDBsum]</span></td></tr>
 </table>
+== Function ==
+[[http://www.uniprot.org/uniprot/OPR1_ARATH 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).<ref>PMID:19605548</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 35: @@
 [[Category: 12-oxophytodienoate reductase]]
 [[Category: Arabidopsis thaliana]]
-[[Category: CESG, Center for Eukaryotic Structural Genomics.]]
+[[Category: Structural genomic]]
-[[Category: Kondrashov, D A.]]
+[[Category: Kondrashov, D A]]
-[[Category: Levin, E J.]]
+[[Category: Levin, E J]]
-[[Category: Phillips, G N.]]
+[[Category: Phillips, G N]]
-[[Category: Wesenberg, G E.]]
+[[Category: Wesenberg, G E]]
-[[Category: Center for eukaryotic structural genomic]]
 [[Category: Cesg]]
 [[Category: Ensemble refinement]]
 [[Category: Plant protein]]
-[[Category: Protein structure initiative]]
+[[Category: PSI, Protein structure initiative]]
-[[Category: Psi]]
 [[Category: Refinement methodology development]]
-[[Category: Structural genomic]]

2q3r

From Proteopedia

Revision as of 14:44, 25 December 2014

Ensemble refinement of the protein crystal structure of At1g76680 from Arabidopsis thaliana

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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