Fellow’s research: Discovery of a new class of enzymes with important function in metabolism


27 Sep 2019

Fellow’s research: Discovery of a new class of enzymes with important function in metabolism

 

Dr Siddhesh S. Kamat, Intermediate Fellow

Indian Institute of Science Education and Research (IISER), Pune

In our recently published study in Biochemistry, we describe the unmet need for developing methods to assign functions to proteins of unknown function, and in doing so, define the function of the orphan serine hydrolase enzyme ABHD14B as a novel lysine deacetylase (KDAC) that is involved in numerous physiological processes.

The graphical abstract

The tremendous technological progress in the process of decoding the complete DNA sequence of an organism, i.e. genome sequencing, has resulted in an explosion in the number of available protein sequences. This has concomitantly led to the propagation of errors in defining the function for enzyme or a lack of known functions for them. The problem, in particular, exists in databases that rely heavily on high-throughput, computational predictions of enzyme function without experimental verification. In this post-genomic era focussed on putting the information encoded in the genomic text to use, this conundrum presents modern biochemists with challenges in studying enzyme mechanisms and understanding their endogenous functions.

We are interested in annotating function to members of the metabolic serine hydrolase enzyme family, as these enzymes play important roles in metabolism and biological signalling, and their deregulation results in several human diseases. The metabolic serine hydrolase family consists of approximately 125 enzymes, of which, 50% lack function assignment, and the (a/b)-hydrolase domain protein # 14B (ABHD14B) is an example of such an unannotated serine hydrolase enzyme.

About a decade ago, ABHD14B was identified as an interactor of the conserved histone acetyl-transferase domain of the largest subunit of the Transcription Factor II D (CCG1/TAFII250) and was thus named as CCG1/TAFII250-interacting factor B (CIB). Following up on this initial discovery, human ABHD14B was purified and shown to have weak hydrolase activity for a surrogate substrate. The three-dimensional structure of this enzyme was elucidated over a decade ago, yet, the endogenous substrates (produced/present in vivo) and the biological pathways that ABHD14B governs in vivo have remained cryptic to date.

Our main objective for this study was to assign function to ABHD14B, and prospect the biological pathways that it might regulate. In this study, we report the development of several biochemical assays and a much-needed, selective ABHD14B-antibody, and the use of these tools in conjunction with cell biology and mass spectrometry, in annotating ABHD14B as a novel lysine deacetylase (KDAC). We showed this enzyme’s ability to transfer an acetyl group from an acetylated-lysine (acetyl-derivative of the amino acid lysine) residue of a protein to co-enzyme A (CoA), and make the important biological metabolite acetyl-CoA in the process. To better understand this enzymatic transformation, we collaborated with the Jennifer Bridwell-Rabb’s lab from the University of Michigan, and were able to provide a structural basis for this exciting metabolic reaction.  

Taken together, our annotation of ABHD14B not only identified the function and thus “deoprhanizes” a metabolic serine hydrolase enzyme, but also adds a third family to the repertoire of enzymes that are capable of transferring the acetyl group from post-translationally modified protein lysine residues in addition to the well-studied sirtuins and histone deacetylases. Publicly available databases and other genomic studies on large populations have recently shown that the deregulated (over)expression of ABHD14B is linked to progression and pathogenesis of aggressive cancers in humans, and thus from a biomedical perspective, finding out the biological pathways that ABHD14B influences would add to our current understanding of cancer malignancy.

Reference:

Functional annotation of ABHD14B, an orphan serine hydrolase enzyme. Abinaya Rajendran1,*, Kaveri Vaidya1, Johnny Mendoza, Jennifer Bridwell-Rabb, Siddhesh S. Kamat*, Biochemistry, September 2019.

1These authors contributed equally to this work, *co-corresponding authors

Banner Image Credits: Crystal structure of the human CCG1/TAFII250-interacting factor B (CIB); DOI: 10.2210/pdb1IMJ/pdb