I agree wholeheartedly with Wenhua - one can never divine someone's intentions from a map and model.However, I think that it is reasonably clear that there are some issues with the ligands in this structure, especially in chain A.If this were me, I think that I might be moved to write this up in a letter to the editor of the journal and perhaps submit the re-refined model to the PDB, for all the world to see?DI guess we should be careful of using 'fabrication' and 'lie' when referring others' work. It either could be a 'biased interpretation', provided you are right in this case.WenhuaFor what reason are you soliciting opinions?
JPK
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of James Woo
Sent: Wednesday, January 20, 2016 1:34 PM
To: [log in to unmask]
Subject: [ccp4bb] questionable structures
Dear All,
I saw a paper published recently on JBC (http://www.jbc.org/content/early/2015/12/14/jbc.M115.699801.long). The authors reported the structures of cyclic di-AMP degradation enzyme Rv2837c (apo and complex with its catalytic intermediate pApA; this phosphodiesterase can convert c-di-AMP into two 5’ AMP and also can degrade linear pApA into two 5’AMP.) and gave a hydrolysis mechanism which the authors claimed it is a novel one. However, when downloaded the PDB file- 5CET (Apo Rv2837c) and 5CEU (Rv2837c-pApA)-provided by the authors and refined them, there are questions within these two structures.
As for the apo structure, there are lots of positive densities in the catalytic center which is apparently a tetrahedral anion, for which the author simply assigned several waters.
As for the complex structure, there are two protein molecules (A and B) in the Asymmetric cell, the author assigned two pApA, the intermediate of the reaction from c-di-AMP to 5’AMP. In B molecule, the author added one water between metal ion (manganese) and phosphorus of pApA (but in A molecule no such water) and claim this is the reactive water which can attack the phosphorus of pApA. However, closed examining the structure, one can find this water is questionable. After refinement, this water expel the phosphorus of pApA away from the metal ion leading negative and positive electron density around the active center. More surprisingly, the ligands assigned by the author are also questionable, may not be pApA. Removing this doubtable water and pApA in B molecule, using two 5’AMP instead and refinement, one can find it is clear the two 5’AMP are very comfortable there and also for the case in A molecule.
In fact, the catalytic mechanism claimed by the author is nothing new. Look at this paper published in nature 2009(http://www.nature.com/nature/journal/v459/n7249/full/nature07966.html), which give us a detailed mechanism for this two manganese ions degrading cyclic di-GMP. But in this JBC paper, it seems that the authors want to follow this nature paper’s mechanism and fabricated this reaction water awkwardly. Also, the author did not cite the work presented by this nature paper. The authors may tell the readers a lie in their paper.
I attached the pictures before and after ligand change. How about your opinions about these two structures? Can you ccp4bbee judge it and give some suggestions on what is the density in the active site of apo structure and how to definitely identify the ligands in the complex? Thank you so much!
best,
James
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David Briggs
about.me/david_briggs