The Importance of Oxidation in VCTLCSC

Just before my sabbatical on this blog, I was looking at the length of bonds which linked the metal to the sulphurs of the cysteine residues to test the state of evidence in the small molecule cystallographic record on how oxidation might change such bond lengths. There wasn't much data around for Co and Fe based systems to draw many inferences from. However, a new paper is just out looking at a model system based around Ru which has been synthesized in the various oxidation states of sulphur with the hope of giving some clues on what sulphur oxidation might offer to NHases.

Influence of Sequential Thiolate Oxidation on a Nitrile Hydratase Mimic Probed by Multiedge X-ray Absorption Spectroscopy by Jason Shearer, Paige E. Callan, César A. Masitas, and Craig A. Grapperhaus in Inorganic Chemistry (DOI: 10.1021/ic202453c).

They use a range of techniques including multiedge X-ray absorption spectroscopy and some serious hardcore DFT calculations to look at/predict how ionic and how Lewis acidic the complexed metal becomes as the sulphur ligands are sequentially oxygenated. Basically you get a harder Lewis acid as you move from naked sulphur through to a mixed sulfenato/sulfinato species. As the abstract graphic shows....

In the final few paragraphs, they speculate what this means for the mechanism of nitrile hydratase hydration (they say "hydrolysis" but that means the complete breaking up the whole bond to acid and ammonia in my book, not just breaking a couple of pi bonds with a molecule of water.). They show versions of the two most commonly proposed models- metal-bound hydroxide attacking a free floating nitrile, and metal-bound nitrile getting walloped by a hydroxide. They suggest that increasing hardness of the metal centre should favour the attachment of an oxygen based ligand over the nitrogen of a nitrile, and hence favour the metal bound hydroxide model. They end with the comment that harder Lewis acidity would actually aid NHase catalysis whatever was bound to the metal. 

How widespread are NHases in eukaryotes?

There is a neat diagram summarizing the findings of the paper by Marron, Akram and Walker called "Nitrile Hydratase Genes Are Present in Multiple Eukaryotic Supergroups" in PLoS One to be found here in full. There is quite a lot of legend that goes with it that I recommend you look at the paper for, but crucially asterisk * means evidence of one eukaryotic NHase subunit (and hence ** means evidence of both), and hash # means a dodgy read more suggestive of prokaryotic contamination.

So that's a black mark for any NHase in plants and animals then...

NHase in harmful algal blooms

Last year I put up a blogpost about finding what looked like the alpha chain of a nitrile hydratase in the eukaryote Aurecococcus anophagefferens which is something that makes up brown tide algal blooms. The paper that introduces the genomic data which provided my hit back then is

Christopher Gobler, Dianna Berry, Sonya Dyhrman, and Steven Wilhelm. "Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics" Proceedings of the National Academy of Sciences of the USA 108.11 (2011): 4352-4357

This little beastie has a whole load of enzymes involved in degrading organic nitrogen containing compounds. The authors of the paper suggest that since it lives in an ecological niche which is typically low in organic nitrogen but high in organic nitrogen so having a suite of enzymes to harvest nitrogen from organics is a strategy to give a competitive advantage over other phytoplankton which don't have this ability. There is a supplemental figure which shows the list of these enzymes and whether competing species have them. A rough cut and paste below shows that it is really out on its own from this data.

This organism also seems to be a Guinness world record holder for the number of selenium containing proteins in its proteome (56). Interesting but not entirely relevant for this blog!

How have the database numbers changed in a year?

Last year I did a quick text search for "nitrile hydratase" as a search term under proteins on the NCBI website. This gave me 2869, of which 1042 were RefSeq data. Today when I checked there are 3573 (+25%), of which 1369 (+31%) were RefSeq.
No new PDB files have been deposited of nitrile hydratases since March 2011 which was the NHase from Pseudomonas putida.

New paper on eukaryotic nitrile hydratases

One of the things that has refocussed me on NHases is the new paper in PLoS ONE on eukaryotic nitrile hydratases. It looks fascinating on a brief flick through.

Nitrile Hydratase Genes Are Present in Multiple Eukaryotic Supergroups by Alan O. Marron, Michael Akam and Giselle Walker in PLoS ONE here.

They have found more single subunit NHases in small eukaryotes, and discount their presence in anything bigger than a protist (like the ones in Ricinus communis) as prokaryotic contamination.

I'll be having a good perusal of this paper.

It's been a while...

I have been concentrating on my other research interests recently (anti-fouling surfaces, paint analysis and mass spectrometry as it happens) so I haven't updated this blog for a couple of months. I have had one student (Hello Luke!) working away on NHases, and he reckons that two of our NHases (including the one from Monosiga brevicollis) can monohydrate a substituted malonitrile.

S-M bond lengths

I was wondering what a "normal" bond length might be for a thiol to iron or cobalt might be, and then what might happen to that bond length might do if that bond was oxidized once and then twice. The best way to do this is to look at the small molecule crystallographic data so I got my friend Ross to comb through the usual database to find examples of the various bonding motifs.

It turns out that there are no examples of 1b in the CCD, and precious few of 1c (only 4), 2b (only 5) and 2c (a more respectable 15). There are loads of examples of 1d (actually 286) and 2d (102).
Anyway, there isnt much of a difference in average bond lengths between these types: 1c- 2.221 angstroms, 1d- 2.276 angstroms, 2b- 2.225 angstroms, 2c- 2.208 angstroms and 2d- 2.252 angstroms.
Here are a few histograms showing the distributions that lie behind these means.