The paper that goes with 3QXE

The paper which describes the work that lead to the pdb file 3QXE and its mutant brethren has just been put up as an accepted manuscript for the ACS journal, Biochemistry. Its corresponding authors are Mary Jo Ondrechen and Dagmar Ringe, and it goes by the inviting title of "Evidence for Participation of Remote Residues in the catalytic activity of Co-type Nitrile hydratase from Pseudomonas putida". They have been looking at which residues in the outer shells around the active site influence activity.

PDBs on a phylogenetic tree

There is a figure of a phylogenetic tree in the Prasad Balla review from 2010 which gives a separation of the different currently known sequences. I have very roughly stitched the tree together from the two parts given on two pages of the review and then I have dropped on top the rough positions of the three most distinct cobalt centred PDB files (1V29, 1UGP and 3QXE) and one of the rhodococcus iron centred files (1AHJ). It is interesting that workers seem to be producing PDB files solely from the right hand half of this tree.

3QXE- the new NHase pdb file- from Pseudomonas putida

I thought I'd have a look to see how different the new pdb file was from those already in the public domain.
First of all a ClustalW alignment of the alpha chains shows that it has a score of 52 with 1V29 and a score of 54 with 1UGP. (For reference, 1V29 and 1UGP have a score of 59 between them). The numbers might not be completely robust because I note that the modified cysteines are not dealt with the same in the three amino acid sequences. The central portions of the sequence are very similar, with most of the diversity at the ends (see below: 1V29 then 1UGP and finally 3QXE)

Using DeepView's RMS measure of 3D similarity after an Iterative Magic Fit of  the new pdb with the files for 1V29 and 1UGP enzymes you get two numbers of approximately 1-1.05 (for reference between 1V29 and 1UGP the value is 1.15). This all suggests that this new file describes a new distinct structural arrangement.

But which is more popular nitrilase or nitrile hydratase?

Google have a rather entertaining Google Labs product called the NGram viewer where they allow you to check the ranking of the number of times that books published in a specific year use words which you define. Their examples are like "nursery school" versus "kindergarten". I thought it might be rather more relevant for this blog to try "nitrilase" against "nitrile hydratase".

NGram viewer- nitrilase v nitrile hydratase

Basically nitrilase has been more popular apart from a burst of enthusiasm for NHase between 1988 and 1994, and a photofinish victory in 2003.

NCBI- April numbers for NHase

A quick text search for "nitrile hydratase" under proteins on NCBI's website shows 2827 (+150 in a month!) hits for the phrase, and 1023 (+35 since the start of March) RefSeq hits. The number of PDB hits is up 5 to 41, as a new crystal structure from the cobalt centred NHase from Pseudomona putida has been uploaded along with the data for four point mutants of it.

Looking at the NHase from Monosiga brevicollis

I have been looking at the sequence for the single subunit NHase from the eukaryote Monosiga brevicollis. There are four things that spring to mind of interest:
1. The thing has joined the two prokaryotic subunits together in the fashion B to A.
2. The usual signature bit of the sequence says it is a cobalt centred NHase, and the alpha subunit is very similar to that shown by the two cobalt centred NHases with pdb files 1V29 and 1UGP.

 3. The joint between the alpha and beta subunits has a LOT of histidines in it, which explains why it took a long time to come off the nickel affinity column!

4. The surface loop which is nice differentiating feature between cobalt-centred and iron centred NHase (which dont have it) is very different with this beast. The picture below is of 1V29, with the loop indicated.