I am desperately searching for an anabolic enzymatic reaction, ideally with a metal ion involved in the reaction complex, and for which -- unlike in the case of the lactose synthase -- we have snapshots for the critical step of the reaction in PDB that shows the alignment of the two ligands which get bonded into a single stereo-isomer. It's not easy by just fishing in UniProt because most PDB entries do not have ligands, and when they have, as with lactose synthase, then they don't have both ligands shown. I know this is very difficult to capture these precise moments in a reaction, which is why I am asking this question as there may be only a single or a hand full of such PDB entries in millions -- a literal needle in the haystack. I would take a best guess predicted model also, don't care if it is actually seen in x-ray imaging, as long as it has a PDB entry.

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    $\begingroup$ How about the active site of myosin with MgATP present? $\endgroup$ Oct 1, 2021 at 18:29
  • $\begingroup$ @ToddMinehardt, that seems to be what the doi:10.1107/S0108767309054361 discusses as one example, but I want an anabolic reaction, some synthase, to show how one stereo-isomer is produced and not the other. $\endgroup$ Oct 1, 2021 at 18:48
  • $\begingroup$ sciencedirect.com/science/article/pii/S0969212603001680 $\endgroup$
    – Karsten
    Oct 2, 2021 at 11:05

1 Answer 1


When an enzymatic reaction is studied using X-ray crystallography, there are multiple structures that provide information:

  1. The apo-enzyme (empty active site)
  2. Enzyme with inhibitor in the active site
  3. Product complex
  4. Substrate complex

Of those four types, (4) is often the most difficult to achieve. The first enzyme studyied by crystallography, lysozyme, still lacks a substrate complex structure as far as I know. The reason this is difficult is that crystallographic data collection takes time, and during that time the substrate will react. Strategies to still get information about the substrate complex are to use an active-site mutant (inactivated enzyme), to leave out substrates in multi-substrate reactions, or to work with caged substrates (e.g. caged ATP) and time-resolved crystallography.

To search for a stereospecific enzyme, you could go after reactions that have two possible ways of connecting two substrates (e.g. synthesis of lactose vs maltose, search for retention vs. inversion of configuration) or substrates that have a prochiral center (e.g. in the reaction of pyruvate to lactate). Often, textbooks will choose a system that is structurally well characterized to illustrate the stereospecific of enzymes, so looking in the table of contents of textbooks on enzyme mechanism might also be a search strategy.

Lactate dehydrogenase comes close to your list of requirements. In the reverse direction, it transforms pyruvate with its prochiral center stereospecifically to lactate.

The mechanism is described here and depicted here. Multiple structures with pyruvate exist, as listed here. If this is not a good example for the OPs needs, use the same kind of search strategies to find other examples.

It is likely that for a complete view of an enzymatic mechanism (which is just a hypothesis in any case) you would have to combine information from multiple structures.

  • $\begingroup$ Thank you for your explanations and links to the LDH. Indeed this is very close to what I was looking for! Thank you, thank you! $\endgroup$ Oct 2, 2021 at 15:08

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