Naturally occurring circular permutations in proteins

Uliel, Shai; Fliess, Amit; Unger, Ron

doi:10.1093/protein/14.8.533

Cited by 50 publications

(60 citation statements)

References 15 publications

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“…In both cases various intermediate forms must have existed during evolution. The requirement that such intermediate forms are stable and should offer some form of advantage to the organism to prevent removal from the gene pool, can explain why the number of circular permutations observed in proteins is rather small (30).…”

Section: Resultsmentioning

confidence: 99%

Crystal structure of a 117 kDa glucansucrase fragment provides insight into evolution and product specificity of GH70 enzymes

Vujicic-Zagar

Pijning

Kralj

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

151

262

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Glucansucrases are large enzymes belonging to glycoside hydrolase family 70, which catalyze the cleavage of sucrose into fructose and glucose, with the concomitant transfer of the glucose residue to a growing α-glucan polymer. Among others, plaque-forming oral bacteria secrete these enzymes to produce α-glucans, which facilitate the adhesion of the bacteria to the tooth enamel. We determined the crystal structure of a fully active, 1,031-residue fragment encompassing the catalytic and C-terminal domains of GTF180 from Lactobacillus reuteri 180, both in the native state, and in complexes with sucrose and maltose. These structures show that the enzyme has an α-amylase-like ðβ∕αÞ 8 -barrel catalytic domain that is circularly permuted compared to the catalytic domains of members of glycoside hydrolase families 13 and 77, which belong to the same GH-H superfamily. In contrast to previous suggestions, the enzyme has only one active site and one nucleophilic residue. Surprisingly, in GTF180 the peptide chain follows a "U"-path, such that four of the five domains are made up from discontiguous N-and C-terminal stretches of the peptide chain. Finally, the structures give insight into the factors that determine the different linkage types in the polymeric product.crystal structure complexes | exopolysaccharide | Lactobacillus reuteri | dental caries

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Section: Resultsmentioning

confidence: 99%

Crystal structure of a 117 kDa glucansucrase fragment provides insight into evolution and product specificity of GH70 enzymes

Vujicic-Zagar

Pijning

Kralj

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

151

262

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“…A common approach to the study of protein folding and the significance of secondary structure topology is the creation of circularly permuted forms of the proteins in question (26). Usually in this approach the original N and C termini are brought together with a linker peptide, whereas the new termini are typically introduced into a loop region.…”

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confidence: 99%

Construction of a Dual Chain Pseudotetrameric Chicken Avidin by Combining Two Circularly Permuted Avidins

Nordlund

Laitinen

Hytönen

et al. 2004

Journal of Biological Chemistry

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Two distinct circularly permuted forms of chicken avidin were designed with the aim of constructing a fusion avidin containing two biotin-binding sites in one polypeptide. The old N and C termini of wild-type avidin were connected to each other via a glycine/serine-rich linker, and the new termini were introduced into two different loops. This enabled the creation of the desired fusion construct using a short linker peptide between the two different circularly permuted subunits. The circularly permuted avidins (circularly permuted avidin 5 3 4 and circularly permuted avidin 6 3 5) and their fusion, pseudotetrameric dual chain avidin, were biologically active, i.e. showed biotin binding, and also displayed structural characteristics similar to those of wild-type avidin. Dual chain avidin facilitates the development of dual affinity avidins by allowing adjustment of the ligand-binding properties in half of the binding sites independent of the other half. In addition, the subunit fusion strategy described in this study can be used, where applicable, to modify oligomeric proteins in general.

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“…The present computational internal sequence repeats analysis provides a systematic analysis of the extensin-1 and extensin-2 family in a significant dataset by considering previous studies 17,18,22,23 explaining the accelerated evolution and the role of these proteins in abiotic stresses, like gravitational stress in both herbs and trees and tension wood formation in trees, and biotic stress, like pathogenic resistance.…”

Section: Resultsmentioning

confidence: 99%

“…In other words, circular permutation in a protein means that the N-terminus of one protein is similar to the C-terminus of the other and vice versa. [23][24][25] The permuted regions may cover a significant portion of both proteins, be within a partial region of the protein, or may be present in two proteins of very different lengths. 23 Studies of circular permutation are useful in many protein engineering and protein folding experiments.…”

mentioning

confidence: 99%

“…[23][24][25] The permuted regions may cover a significant portion of both proteins, be within a partial region of the protein, or may be present in two proteins of very different lengths. 23 Studies of circular permutation are useful in many protein engineering and protein folding experiments. 26,27 Various researchers [27][28][29] have reported the existence of circular permutation in many biological sequences and structures, including some carbohydrate-related enzymes and binding proteins, swaposins, transaldolases, FMN-binding proteins, glutathione synthetases, methyltransferases, ferredoxins, and protease inhibitors.…”

mentioning

confidence: 99%

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Computational internal sequence repeats analysis of accelerated evolution and the role of extensins under abiotic and biotic stresses

Jothi¹,

Parthasarathy²,

Krishnamurthy³

2010

OAB

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Extensins are hydroxyproline-rich glycoproteins present in the plant cell wall. Accelerated evolution and the role of extensins involved in abiotic stresses, like gravitational stress and tension wood formation, and biotic stress, like pathogenic resistance, were investigated through computational internal sequence repeats analysis of their sequences. Multiple sequence alignment analysis of extensin-1 and extensin-2, present in both herbs and trees, was used to investigate their role in gravitational stress and tension wood formation. The role of extensins in pathogenic resistance was investigated by showing the existence of circular permutation in both extensin-1 and extensin-2 sequences between plants of Fabaceae. It was analyzed through Dot plots, and the study predicted that many partial circular permutations exist between sequences of different length. The clustering study of the internal sequence repeats of extensin family through phylogenetic analysis and reconstruction of patterns of repeat identities between sequences showed that unequal crossover exists in extensin-2. From the existence of unequal crossover nature in the circularly permuted extensin-2, accelerated evolution is indicated by the pattern of repeats in herbaceous plants of the Fabaceae family and trees of different taxa, in addition to pathogenic resistance.

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Naturally occurring circular permutations in proteins

Cited by 50 publications

References 15 publications

Crystal structure of a 117 kDa glucansucrase fragment provides insight into evolution and product specificity of GH70 enzymes

Crystal structure of a 117 kDa glucansucrase fragment provides insight into evolution and product specificity of GH70 enzymes

Construction of a Dual Chain Pseudotetrameric Chicken Avidin by Combining Two Circularly Permuted Avidins

Computational internal sequence repeats analysis of accelerated evolution and the role of extensins under abiotic and biotic stresses

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