Invariant glycines and prolines flanking in loops the strand β2 of various (α/β)₈‐barrel enzymes: A hidden homology?

Abstract

The question of parallel (a/&barrel fold evolution remains unclear, owing mainly to the lack of sequence homology throughout the amino acid sequences of (a/P),-barrel enzymes. The "classical" approaches used in the search for homologies among (cu/@),-barrels (e.g., production of structurally based alignments) have yielded alignments perfect from the structural point of view, but the approaches have been unable to reveal the homologies. These are proposed to be "hidden" in (a/P),-barrel enzymes. The term "hidden homology" means that the alignment of sequence stretches proposed to be homologous need not be structurally fully satisfactory. This is due to the very long evolutionary history of all (a//3)8-barrels. This work identifies so-called hidden homology around the strand 02 that is flanked by loops containing invariant glycines and prolines in 17 different (a/P),-barrel enzymes, i.e., roughly in half of all currently known (a/&-barrel proteins. The search was based on the idea that a conserved sequence region of an (a/P),-barrel enzyme should be more or less conserved also in the equivalent part of the structure of the other enzymes with this folding motif, given their mutual evolutionary relatedness. For this purpose, the sequence region around the well-conserved second 0-strand of a-amylase flanked by the invariant glycine and proline (56&GFTAIWITP, Aspergillus oryzae a-amylase numbering), was used as the sequence-structural template. The proposal that the second 0-strand of (a/P),-barrel fold is important from the evolutionary point of view is strongly supported by the increasing trend of the observed 02-strand structural similarity for the pairs of (oc/fl),-barrel enzymes: a-amylase and the a-subunit of tryptophan synthase, a-amylase and mandelate racemase, and a-amylase and cyclodextrin glycosyltransferase. This trend is also in agreement with the existing evolutionary division of the entire family of (a/P),-barrel proteins.

Structure of the human glycogen‐associated protein phosphatase 1 regulatory subunit hGM: Homology modeling revealed an (α/β)8‐barrel‐like fold in the multidomain protein

“…Altogether, the conserved sequential distribution of patterns suggests that all members of the subset of glycogen-associated PP1 regulatory subunits studied here share a common fold: like hGM, they may possess an~a0b! 8 -barrel-like fold very often encountered in starch and polysaccharide-related enzymes~Farber & Petsko, 1990;Jespersen et al, 1993;Janecek, 1996!. This fold has been shown in this work to be consistent with PP1C anchoring and glycogen interaction, both processes being predominantly controlled by hydrophobic forces deriving from F660V64 and V1480 F1530V157~hGM numbering!, respectively.…”

Studies on a Tyr residue critical for the binding of coenzyme and substrate in mouse 3(17)α-hydroxysteroid dehydrogenase (AKR1C21): structure of the Y224D mutant enzyme

“…Sequence-alignment comparisons of various AKRs revealed that the amino-acid sequences forming the barrel are well conserved compared with those forming the loop regions. The conserved regions seemingly maintain the architecture of the barrel, while residues belonging to the loop regions discriminate between several structurally related substrates and act as specificity determinants (Matsuura et al, 1998;Janecek, 1996;Jez et al, 1997). The reactions catalyzed by AKR enzymes follow an ordered bi-bi mechanism in which the coenzyme binds first and leaves last.…”