Supplementary material
Assessments of full-length structures of hydrolases
According to the Pfam database1, the six hydrolases examined in this study are parts
of the full-length proteins. This means it is possible that the remaining part of the
protein could cover the ligand molecules, as in the cases of the transferases. We
examined this possibility in this section.
The full-length forms of the two hydrolases, cathepsin S in the ‘cysteine proteinases’
(d.3.1)
superfamily and carboxypeptidase A in the ‘Zn-dependent exopeptidases’
(c.56.5) superfamily, are proenzymes. Thus, the active forms lack the additional
domains. In the cases of mRNA decapping enzyme in the ‘HIT-like’ (d.13.1)
superfamily and tyrosyl-DNA phosphodiesterase in the ‘phospholipase D/nuclease’
(d.136.1) superfamily, the structure-unknown domains are at the N-termini, but they
were predicted to be intrinsically disordered by DISOPRED22. Considering the length
of the disordered region and the position of the N-terminus in the crystal structures, we
suppose that they have no influence on the ligand molecules. M-phase inducer
phosphatase 2 of the ‘rhodanese/cell cycle control phosphatase’ (c.46.1) superfamily
also has a structure-unknown region at the N-terminus. DISOPRED2 predicted a
disordered structure of about 100 residues adjacent to the catalytic domain in the
sequence. For the remaining 300 residues, we attempted fold recognition by 3D-jury3.
However, the prediction result was not significant, suggesting at least that the
N-terminal domain may have a different architecture from that of the corresponding
transferase, carboxymethylated rhodanese, contributing to the insulation of the ligand.
Lon protease, of the ‘ribosomal protein S5 domain 2-like’ (d.14.1) superfamily, was
discussed in the Results section.
1
Transferases lacking clear evidence of insulation
In three out of the 15 superfamilies, the structural features that differentiate the
transferases and hydrolases were not identified. In the ‘alpha/beta-hydrolases (c.69.1)’
and ‘pentein (d.126.1)’ superfamilies, peripheral regions cover the ligand molecules in
the transferases. However, some of the hydrolases in those superfamilies also possess
peripheral regions, which are not always identical to those of the transferases, and cover
the ligand molecules. The hydrolases in the ‘alpha/beta-hydrolases’ superfamily
reportedly exhibit dynamic properties to supply water to the buried ligand molecules,
such as the presence of a water tunnel4 and a conformational change to the open
structure5,6. In the ‘glycoside hydrolase/deacetylase (c.6.2)’ superfamily, a transferase,
4-alpha-glucanotransferase, catalyses the degradation of amylose, a polysaccharide
composed of many glucose units. The catalytic residues act on the glycosidic linkage
between the two glucose units of amylase, and the catalysed portion may be covered by
the protein and the adjoining glucose units7. Thus, the ligand molecule itself may
contribute to the insulation in this transferase.
References
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