The Structure of a Truncated Phosphoribosylanthranilate Isomerase Suggests a Unified Model for Evolution of the (βα)8 Barrel Fold

Setiyaputra, Surya; Mackay, Joel P.; Patrick, Wayne M.

doi:10.1016/j.jmb.2011.02.048

Cited by 18 publications

(18 citation statements)

References 53 publications

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“…This is in agreement with hypotheses on the origin of the (βα) 8 barrel fold [22]. One hypothesis suggests that they have evolved by tandem duplication and fusion of an ancestral half-barrel [20].…”

Section: Discussionsupporting

confidence: 91%

“…The existence of natural proteins containing the (βα) 7 subdomain suggests that the splice variants resulting in this subdomain can retain a soluble and stable structure. The experimental existence of smaller substructures in the folding process and soluble and stable subdomains formed by (βα) 2 , (βα) 4 , (βα) 5 or (βα) 6 have been demonstrated in different (βα) 8 barrel proteins [20]–[22], [28], [29]. Structural and functional resilience towards substitutions of βα subdomains and βα-loops have also been demonstrated in this fold [24]–[26], [32] which is in agreement with our observations of resilience to β-strand substitutions.…”

Section: Discussionmentioning

confidence: 99%

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Alternative Splice Variants in TIM Barrel Proteins from Human Genome Correlate with the Structural and Evolutionary Modularity of this Versatile Protein Fold

et al. 2013

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After the surprisingly low number of genes identified in the human genome, alternative splicing emerged as a major mechanism to generate protein diversity in higher eukaryotes. However, it is still not known if its prevalence along the genome evolution has contributed to the overall functional protein diversity or if it simply reflects splicing noise. The (βα)8 barrel or TIM barrel is one of the most frequent, versatile, and ancient fold encountered among enzymes. Here, we analyze the structural modifications present in TIM barrel proteins from the human genome product of alternative splicing events. We found that 87% of all splicing events involved deletions; most of these events resulted in protein fragments that corresponded to the (βα)2, (βα)4, (βα)5, (βα)6, and (βα)7 subdomains of TIM barrels. Because approximately 7% of all the splicing events involved internal β-strand substitutions, we decided, based on the genomic data, to design β-strand and α-helix substitutions in a well-studied TIM barrel enzyme. The biochemical characterization of one of the chimeric variants suggests that some of the splice variants in the human genome with β-strand substitutions may be evolving novel functions via either the oligomeric state or substrate specificity. We provide results of how the splice variants represent subdomains that correlate with the independently folding and evolving structural units previously reported. This work is the first to observe a link between the structural features of the barrel and a recurrent genetic mechanism. Our results suggest that it is reasonable to expect that a sizeable fraction of splice variants found in the human genome represent structurally viable functional proteins. Our data provide additional support for the hypothesis of the origin of the TIM barrel fold through the assembly of smaller subdomains. We suggest a model of how nature explores new proteins through alternative splicing as a mechanism to diversify the proteins encoded in the human genome.

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Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Alternative Splice Variants in TIM Barrel Proteins from Human Genome Correlate with the Structural and Evolutionary Modularity of this Versatile Protein Fold

et al. 2013

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“…However, huge number of proteins with the ( ) 8 fold exist, so the folding mechanisms of ( ) 8 proteins may show wide variations. Actually, various folding mechanisms of ( ) 8 proteins have been reported (Akanuma & Yamagishi, 2008;Gu et al, 2007;Silverman & Harbury, 2002;Seitz at al., 2007;Setiyaputra et al (2011)). Such variation of folding may be related to the nonrobustness of the second and third common folding units in HisF and HisA.…”

Section: Discussionmentioning

confidence: 99%

“…On the other hand, the NMR study by Setiyaputra et al (2011) demonstrated that the truncated phosphoribosylanthranilate isomerase (trPRAI), which is three-quarter-barrelsized fragment of a ( ) 8 barrel, forms the distinct 3D structure (Setiyaputra et al, 2011). This observation may suggest that the ( ) 2 quarter-barrel is a kind of structural module in a ( / ) 8 barrel protein but all 4 modules are not always indispensable.…”

Section: Wwwintechopencommentioning

confidence: 99%

Analyses of Sequences of (β/α) Barrel Proteins Based on the Inter-Residue Average Distance Statistics to Elucidate Folding Processes

Matsuoka¹,

Kabata²,

Kawai³

et al. 2012

Chemical Biology

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“…This 2-fold symmetry has also been observed in the solved structures of the PriA enzymes from Streptomyces coelicolor (ScPriA) and Mycobacterium tuberculosis (MtPriA), the C. efficiens subHisA, and also TmHisF, the homologous (␤␣) 8 barrel that catalyzes the subsequent step in histidine biosynthesis (4, 5, 8 -10). However, TrpF does not possess the same symmetrical architecture (11,12).…”

Section: Barrel Enzyme Hisa or Nј-[(5ј-phosphoribosyl)-mentioning

confidence: 99%

Two-step Ligand Binding in a (βα)8 Barrel Enzyme

Söderholm

Guo

Newton

et al. 2015

Journal of Biological Chemistry

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Background: HisA catalyzes a ring-opening isomerization reaction in histidine biosynthesis. Results: Catalytic residues and conformational changes upon substrate binding are clarified by structures, kinetics, and mutagenesis. Conclusion: Closing of active site loops in HisA brings the substrate into a product-like conformation before catalysis. Significance: This exemplifies coupled conformational changes in a (␤␣) 8 barrel enzyme and its substrate and clarifies the mechanistic cycle of HisA.

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The Structure of a Truncated Phosphoribosylanthranilate Isomerase Suggests a Unified Model for Evolution of the (βα)8 Barrel Fold

Cited by 18 publications

References 53 publications

Alternative Splice Variants in TIM Barrel Proteins from Human Genome Correlate with the Structural and Evolutionary Modularity of this Versatile Protein Fold

Alternative Splice Variants in TIM Barrel Proteins from Human Genome Correlate with the Structural and Evolutionary Modularity of this Versatile Protein Fold

Analyses of Sequences of (β/α) Barrel Proteins Based on the Inter-Residue Average Distance Statistics to Elucidate Folding Processes

Two-step Ligand Binding in a (βα)8 Barrel Enzyme

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