Bioinformatic analysis of Malate Thiokinase, a key enzyme in the Serine pathway for assimilation of C1 compounds and energy conversion

LÓPEZ, MARÍA BELÉN; GONZALEZ, JAVIER M.

Buenos Aires

Congreso; Biofísica en tiempos de COVID-19 : Primeras Jornadas Virtuales SAB 2020; 2020

Sociedad Argentina de Biofísica

Climate change resulting from the accumulation of greenhouse gases is a matter of global concern. A solution to this problem could be found in Synthetic Biology for the generation of artificial metabolic pathways using enzymes for assimilation of C1 compounds of the Serine pathway present in bacteria of the genus Methylorubrum.Malate thiokinase (MTK) is a heterodimer (α and β subunits) whose family includes ATP-citrate lyases and succinyl-CoA synthetases (SCS). It catalyzes the only phosphorylation step at the substrate level of the Serine pathway, reversibly producing Malyl-CoA, PO43- and ADP from malate, CoA and ATP, the reaction direction depends on the relative concentrations of substrates and products. It is interesting due to its dual function, catalyzing a key step in the assimilation of C1 and having the important and unusual capacity to exchange energy between CoA thioesters and adenylates.In order to infer the structural properties of MTK whose structure has not yet been solved. The enzyme was examined structurally and phylogenetically using: homology modeling, phylogenetic analysis and sequence similarity networks (SSN). The structures modeled for MTKα and MTKβ are acceptable since they presented r.m.s.d values close to zero and more than 90% of residues in favorable regions. SSNs for MTKα and MTKβ were calculated for the Pfam family PF00549. Their sequences were retrieved from UniProt. The phylogenetic trees were generated with the maximum likelihood algorithm RAxML with automatic bootstop criterion. Homology modeling of the 3D structure of M. extorquens MTK was performed with Phyre2, MTKα showed a sequence similarity of 52 % with Sus scrofa SCS, while MTKβ showed a sequence similarity of 55 % with F. tularensis SCS. Looking at the distribution along the SSNs, it is clear that many sequences remain to be functionally characterized. Only 7 nodes have SwissProt descriptions and PDB structures, and they are SCS enzymes, representing 7 out of 3,165 nodes (0.2%). MTKβ subunits are more conserved that MTKα subunits, as inferred from neighborhood connectivity analysis. Besides, genome neighborhood analysis indicates that MTKαβ genes are restricted to relatively few genera like Methylobacterium and Hyphomicrobium. This work was partly funded by grants from ANPCyT PICT 2017-4590 to J.M.G. and CONICET institutional grant PUE 2018-0035.