User:JamesMilnerWhite/sandbox

The Beta link is a motif in proteins and polypeptides consisting of 5 amino acid residues. It is characterized by an overlap of a G1 type beta bulge and a type II beta turn, in which the 3rd and 4th amino acids of the beta-turn are also the bulged-out side of the beta bulge ^[1]^[2]

G1 beta bulges (beta bulges with a glycine as the first residue of the bulged-out side) typically occur in one of two composite situations, either within a beta bulge loop, or as a component of a beta link[2]. The latter commonly occur at the corners or ends of antiparallel beta sheets in proteins and polypeptides. The beta turn is situated perpendicular to the beta-sheet such that the beta link often acts as a join between the beta-sheet and another secondary structure element; sometimes the beta link connects opposite strands at the end of a single beta-barrel^[3].

In serine proteases the eponymous serine is situated within a well-conserved beta link. The serine occurs at residue 2 of the type II beta-turn (with the oxyanion hole or nest (protein structural motif) at residues 0, 1 and 2). The beta link may provide a hydrogen bonded framework to assist the serine to adopt the correct conformation for catalysis. Some “serine proteases” have a cysteine in place of the serine, performing the same catalytic function, and the beta link is conserved in these proteins too^[4].

References

^ Richardson, JS (1978). "The Beta-bulge: A common small unit of nonrepetitive protein structure". Proceeedings of the National Academy of Sciences USA. 75: 2574–2578.
^ Leader, DP (2021). "Identification and characterization of two classes of G1 β-bulge". Acta Crystallographica. D77: 217–223.
^ Leader, DP (2021). "Identification and characterization of two classes of G1 β-bulge". Acta Crystallographica. D77: 217–223.
^ Leader, DP (2021). "The β-link motif in protein architecture". Acta Crystallographica. D77: 217–223.

External links

Motivated Proteins: [1]^[1]

Category:Protein structural motifs

^ Leader, DP; Milner-White EJ (2009). "Motivated Proteins: A web application for studying small common three-dimensional protein motifs". BMC Bioinformatics. 10 (1): 60. doi:10.1186/1471-2105-10-60. PMC 2651126. PMID 19210785.{{cite journal}}: CS1 maint: unflagged free DOI (link)

[1] Richardson, JS (1978). "The Beta-bulge: A common small unit of nonrepetitive protein structure". Proceeedings of the National Academy of Sciences USA. 75: 2574–2578.

[2] Leader, DP (2021). "Identification and characterization of two classes of G1 β-bulge". Acta Crystallographica. D77: 217–223.

[3] Leader, DP (2021). "Identification and characterization of two classes of G1 β-bulge". Acta Crystallographica. D77: 217–223.

[4] Leader, DP (2021). "The β-link motif in protein architecture". Acta Crystallographica. D77: 217–223.

[5] Leader, DP; Milner-White EJ (2009). "Motivated Proteins: A web application for studying small common three-dimensional protein motifs". BMC Bioinformatics. 10 (1): 60. doi:10.1186/1471-2105-10-60. PMC 2651126. PMID 19210785.{{cite journal}}: CS1 maint: unflagged free DOI (link)

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