While am reading about protein sumoylation this morning I got stuck on sumo interaction motifs and consensus motif line. I heard the the word motifs for the first time. What does motifs mean in this context and What does canonical Sumo consensus motif ΨKx(D/E) mean also? Would you please elaborate the formula and thanks in advance.
A motif means a pattern. Since nucleotides and proteins have a sequence, they can have some patterns of sub-sequence that may serve some kind of function. For example TATA box in DNA serves as a promoter element. Similarly proteins can have some sequence motifs that can serve as recognition sites for binding partners (amongst other functions). Similarly there can be structural motifs in proteins, network motifs in big networks etc.
In this case the motif is a sequence motif.
From Gareau and Lima (2010):
Many SUMO-modified proteins identified contain an acceptor Lys within a ψKX(D/E) consensus motif, where ψ is a large hydrophobic residue
This motif serves as a recognition site for the SUMO-Ligase.
X=Any amino acid
From the below figures (Rodriguez et al., 2000), you can observe that ψ can be leucine (L) (original residue in Ran GAP1), isoleucine (I), phenylalanine (F) or valine (V).
I am not sure about the effect of double hydrophobic residues on rate of SUMO conjugation.