Stability, catalytic versatility and evolution of the (βα)8-barrel fold

Höcker, Birte; Jürgens, Catharina; Wilmanns, Matthias; Sterner, Reinhard

doi:10.1016/s0958-1669(00)00230-5

Cited by 87 publications

(114 citation statements)

References 35 publications

Supporting

Mentioning

103

Contrasting

Order By: Relevance

“…Consequently, the structure of the NADP ϩ -flexible subdomain is dynamic in retaining the rigid small ␤ 4 strand. Our results are consistent with the fact that an enzyme needs to be both stable to maintain their native structures and flexible to allow conformational changes during catalysis (36). Considering evolution of enzymes for pH sensitivity, achieved by tuning the local motion (37), the pH-modulated change in motion of the NADP ϩ -flexible subdomain may be achieved through evolution for photosynthesis.…”

Section: Discussionsupporting

confidence: 85%

Cores and pH-dependent Dynamics of Ferredoxin-NADP+ Reductase Revealed by Hydrogen/Deuterium Exchange

Lee

Tamura

Hoshino

et al. 2007

Journal of Biological Chemistry

View full text Add to dashboard Cite

NMR-detected hydrogen/deuterium (H/D) exchange of amide protons is a powerful way for investigating the residuebased conformational stability and dynamics of proteins in solution. Maize ferredoxin-NADP ؉ reductase (FNR) is a relatively large protein with 314 amino acid residues, consisting of flavin adenine dinucleotide (FAD) and nicotinamide adenine dinucleotide phosphate (NADP ؉ )-binding domains. To address the structural stability and dynamics of FNR, H/D exchange of amide protons was performed using heteronuclear NMR at pD r values 8.0 and 6.0, physiologically relevant conditions mimicking inside of chloroplasts. At both pD r values, the exchange rate varied widely depending on the residues. The profiles of protected residues revealed that the highly protected regions matched well with the hydrophobic cores suggested from the crystal structure, and that the NADP ؉ -binding domain can be divided into two subdomains. The global stability of FNR obtained by H/D exchange with NMR was higher than that by chemical denaturation, indicating that H/D exchange is especially useful for analyzing the residue-based conformational stability of large proteins, for which global unfolding is mostly irreversible. Interestingly, more dynamic conformation of the C-terminal subdomain of the NADP ؉ -binding domain at pD r 8.0, the daytime pH in chloroplasts, than at pD r 6.0 is likely to be involved in the increased binding of NADP ؉ for elevating the activity of FNR. In light of photosynthesis, the present study provides the first structure-based relationship of dynamics with function for the FNR-type family in solution.Protein conformations as shown by x-ray crystallography or nuclear magnetic resonance spectroscopy are virtually dynamic entities over various time ranges in solution (1, 2). Clarifying such conformational motions at the level of the atom or residue is essential for understanding the structural stabilities of proteins and the relationships between protein structures and functions (3-5). The hydrogen/deuterium (H/D) 4 exchange of amide protons in backbones has become an important way to address the motions of a protein from small or relatively large scale motions involved in biological functions such as binding of a substrate or releasing a product to much more large scale motions like a global unfolding process (4, 6). Among several approaches, the H/D exchange combined with heteronuclear NMR spectroscopy is the most convenient and powerful way because it can provide residue-specific information for most residues (7). For many globular proteins, this approach has identified protected cores, which are often composed of secondary structures buried inside the molecules and the cooperative interactions with partner molecules (4, 8), leading to allostery (9). Detailed analyses of exchanges in the native state of cytochrome c in the presence of various concentrations of denaturants suggested a pathway to unfolding, in which groups of secondary structural elements (i.e. foldons) are unfolded sequentially through distin...

show abstract

Section: Discussionsupporting

confidence: 85%

Cores and pH-dependent Dynamics of Ferredoxin-NADP+ Reductase Revealed by Hydrogen/Deuterium Exchange

Lee

Tamura

Hoshino

et al. 2007

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…It appears that both HisF and HisA are composed of two structural domains, namely the corresponding N-and C-terminal half-barrels. These results suggest an evolutionary scenario according to which a primordial gene encoding a (␤␣) 4 -half-barrel as a subunit of a homodimeric enzyme was duplicated and fused to yield a monomeric, ancestral (␤␣) 8 -barrel, from which HisF, HisA, and presumably also TrpF evolved by a series of further gene duplication and diversification events (4,11). Moreover, it was postulated that (␤␣) 4 -halfbarrels are independently evolving domains, implying that new (␤␣) 8 -barrels could be generated by mixing and joining (␤␣) 4 half-barrels from an existing pool (18).…”

mentioning

confidence: 74%

“…These results suggest an evolutionary scenario according to which a primordial gene encoding a (␤␣) 4 -half-barrel as a subunit of a homodimeric enzyme was duplicated and fused to yield a monomeric, ancestral (␤␣) 8 -barrel, from which HisF, HisA, and presumably also TrpF evolved by a series of further gene duplication and diversification events (4,11). Moreover, it was postulated that (␤␣) 4 -halfbarrels are independently evolving domains, implying that new (␤␣) 8 -barrels could be generated by mixing and joining (␤␣) 4 half-barrels from an existing pool (18). Along these lines, an extensive search of the Protein Data Bank (www.pdb.org) with HisF-N and HisF-C as queries revealed significant similarities to several (␤␣) 8 -barrel enzymes and to members of the flavodoxinlike fold family, as indicated by sequence identities of up to 22% and Z scores of up to 6.4 (19).…”

mentioning

confidence: 74%

“…The fold of the canonical (␤␣) 8 -barrel consists of a central barrel of eight parallel ␤-strands and eight external ␣-helices. Connecting loops are located at the N-terminal (␣-␤ loops) and Cterminal (␤-␣ loops) face of the barrel (3,4). Although (␤␣) 8 barrel enzymes catalyze a broad range of chemically diverse reactions, their active sites always are located at the C-terminal face of the barrel (5).…”

mentioning

confidence: 99%

“…The goal of the present work was to reconstruct experimentally the postulated evolutionary events that can lead to the generation of new (␤␣) 8 -barrels from existing (␤␣) 4 -half-barrels. To this end, the half-barrel HisF-C was duplicated, fused, and optimized to yield the stable and monomeric HisF-C*C barrel.…”

mentioning

confidence: 99%

See 2 more Smart Citations

Mimicking enzyme evolution by generating new (βα) ₈ -barrels from (βα) ₄ -half-barrels

Höcker

Claren

Sterner

2004

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

Self Cite

View full text Add to dashboard Cite

Gene duplication and fusion events that multiply and link functional protein domains are crucial mechanisms of enzyme evolution. The analysis of amino acid sequences and three-dimensional structures suggested that the (␤␣) 8-barrel, which is the most frequent fold among enzymes, has evolved by the duplication, fusion, and mixing of (␤␣) 4-half-barrel domains. Here, we mimicked this evolutionary strategy by generating in vitro (␤␣) 8-barrels from (␤␣) 4-half-barrels that were deduced from the enzymes imidazole glycerol phosphate synthase (HisF) and N [(5 -phosphoribosyl)formimino]-5-aminoimidazole-4-carboxamide-ribonucleotide isomerase (HisA). To this end, the gene for the C-terminal (␤␣) 4-half-barrel (HisF-C) of HisF was duplicated and fused in tandem to yield HisF-CC, which is more stable than HisF-C. In the next step, by optimizing side-chain interactions within the center of the ␤-barrel of HisF-CC, the monomeric and compact (␤␣) 8-barrel protein HisF-C*C was generated. Moreover, the genes for the N-and C-terminal (␤␣) 4-half-barrels of HisF and HisA were fused crosswise to yield the chimeric proteins HisFA and HisAF. Whereas HisFA contains native secondary structure elements but adopts ill-defined association states, the (␤␣) 8-barrel HisAF is a stable and compact monomer that reversibly unfolds with high cooperativity. The results obtained suggest a previously undescribed dimension for the diversification of enzymatic activities: new (␤␣) 8-barrels with novel functions might have evolved by the exchange of (␤␣) 4-halfbarrel domains with distinct functional properties. chimeric proteins ͉ gene duplication ͉ histidine biosynthesis ͉ TIM-barrel

show abstract

Mechanisms of Protein Evolution and their Application to Protein Engineering

Glasner

Gerlt

Babbitt

2010

Advances in Enzymology - And Related Areas of Molecular Biology

View full text Add to dashboard Cite

Stability, catalytic versatility and evolution of the (βα)8-barrel fold

Cited by 87 publications

References 35 publications

Cores and pH-dependent Dynamics of Ferredoxin-NADP+ Reductase Revealed by Hydrogen/Deuterium Exchange

Cores and pH-dependent Dynamics of Ferredoxin-NADP+ Reductase Revealed by Hydrogen/Deuterium Exchange

Mimicking enzyme evolution by generating new (βα) ₈ -barrels from (βα) ₄ -half-barrels

Mechanisms of Protein Evolution and their Application to Protein Engineering

Contact Info

Product

Resources

About

Stability, catalytic versatility and evolution of the (βα)8-barrel fold

Cited by 87 publications

References 35 publications

Cores and pH-dependent Dynamics of Ferredoxin-NADP+ Reductase Revealed by Hydrogen/Deuterium Exchange

Cores and pH-dependent Dynamics of Ferredoxin-NADP+ Reductase Revealed by Hydrogen/Deuterium Exchange

Mimicking enzyme evolution by generating new (βα) 8 -barrels from (βα) 4 -half-barrels

Mechanisms of Protein Evolution and their Application to Protein Engineering

Contact Info

Product

Resources

About

Mimicking enzyme evolution by generating new (βα) ₈ -barrels from (βα) ₄ -half-barrels