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I'm looking for an Arabidopsis thaliana gene listed in RCSB with a clear mode of function and active site. In addition it needs to have an obvious phenotype when knocked out like severely retarded growth, lethal or near lethal. The gene also has to be exclusive to plants so RNA polymerase wouldn't work. I found this paper in plant physiology but I'm having trouble finding those genes with an obvious active site. Thank you very much

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I can tell you generally how to go about it.

Go to table S2 from the paper and download the spreadsheet. You can search RCSB for each gene symbol. There are 2400 individual genes and there are probably over 1000 alias genes, so that's a lot of searching. You can do this en masse by using a python script and a library like BioPython, or you can put each symbol into the search box at RCSB.org and see if a structure comes up.

You can and should look over that table for phenotypes you think you can actually work with. Many of the phenotypes in the paper might require a microscope or a good deal of experience with arabidopsis. E.g. "Embryo defective; Preglobular / Globular" what does that mean? You can also write the authors for advice but they might be too busy to get back to you.

Cutting down your search like this before you do it would be very helpful. The number of genes with both an accessible phenotype and a structure will probably be a relatively small list (50?).

Relatively few arabidopsis protein structures are solved, so you will have to do homology modeling - aligning any protein structure sequence(s) you find with the A. thaliana sequence, and deciding where the active site or disruptive mutation would be in the plant gene.

Example: CHY1(CoA Ester Hydrolase) must be solved - searching for "CoA Ester Hydrolase" at rcsb I find a three structures. the human structure 2DQZ has a lot of annotation associated with it. This class of enzymes has been studied for a while, so the active site probably has been studied. A pubmed search should give a lead on where the active site research has been done. using BLAST to align the structures to the arabidopsis gene or to all other CoA Ester Hydrolases would be an important step to take too.

Hope this helps.

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