Comparison of super-secondary structures in proteins

Rao, S.T.; Rossmann, Michael G.

doi:10.1016/0022-2836(73)90388-4

Cited by 851 publications

(378 citation statements)

References 19 publications

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Section: Introductionmentioning

confidence: 99%

“…The most widely distributed protein folding motifs are thought to be remnants of most ancient protein architectures [2,3]. In many textbooks, the Rossmann fold is defined as a babab structure in accordance with the original report [1]. However, elucidation of the structures of many dinucleotide binding enzymes revealed a great diversity in the overall structure of the dinucleotide binding domains.…”

mentioning

confidence: 96%

“…There can be up seven strands in one sheet. This domain structure was named "Rossmann fold" after Michael G. Rossmann who first reported it as a common structure in a variety of nucleotide binding proteins, such as lactate dehydrogenase and flavodoxin [1].The Rossmann fold is one of the five most common structural motifs that appear in a myriad of proteins [2,3]. The most widely distributed protein folding motifs are thought to be remnants of most ancient protein architectures [2,3].…”

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confidence: 99%

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Proteopedia: Rossmann fold: A beta‐alpha‐beta fold at dinucleotide binding sites

Hanukoglu

2015

Biochem Molecular Bio Educ

114

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The Rossmann fold is one of the most common and widely distributed super-secondary structures. It is composed of a series of alternating beta strand (b) and alpha helical (a) segments wherein the b-strands are hydrogen bonded forming a b-sheet. The initial beta-alpha-beta (bab) fold is the most conserved segment of Rossmann folds. As this segment is in contact with the ADP portion of dinucleotides such as FAD, NAD, and NADP it is also called as an "ADPbinding bab fold". The Proteopedia entry on the Rossmann fold (Available at: http://proteopedia.org/w/Rossmann_fold) was generated to illustrate several structural aspects of super families of FAD and NAD(P) binding proteins: (1) The coenzymes FAD and NAD(P) share the basic adenosine diphosphate (ADP) structure. (2) The bab fold motif that is common to both FAD and NAD(P) binding enzymes accommodates the common ADP component of these two coenzymes. (3) In both FAD and NAD(P) binding sites, the tight turn between the first b-strand and the a-helix is in contact with the two phosphate groups of ADP. (4) Keywords: protein structure function and folding; enzymes and catalysis; protein design; biochemical evolution; molecular graphics and representations; comparative biochemistryIn a very large superfamily of dinucleotide binding enzymes, the domains that bind a dinucleotide such as FAD, NAD, and NADP share a common super-secondary structure that is partly composed of a series of alternating beta strand (b) and alpha helical (a) segments wherein the b-strands are hydrogen bonded forming a central b-sheet with helices on either side. There can be up seven strands in one sheet. This domain structure was named "Rossmann fold" after Michael G. Rossmann who first reported it as a common structure in a variety of nucleotide binding proteins, such as lactate dehydrogenase and flavodoxin [1].The Rossmann fold is one of the five most common structural motifs that appear in a myriad of proteins [2,3]. The most widely distributed protein folding motifs are thought to be remnants of most ancient protein architectures [2,3]. In many textbooks, the Rossmann fold is defined as a babab structure in accordance with the original report [1]. However, elucidation of the structures of many dinucleotide binding enzymes revealed a great diversity in the overall structure of the dinucleotide binding domains. The major differences among dinucleotide binding domains of proteins include extensive divergence of the primary structure, variable number of b-strands in the complete b-sheet that forms the Rossmann fold, and large variations in the length and secondary structure of the segment that connects the second and third b-strands.The diversity of the Rossmann fold can be illustrated by two enzymes as examples. In dogfish lactate dehydrogenase the NAD binding motif, babab fold, is a continuous 60 residues long segment (PDB ID: 3LDH) [4]. In contrast, in yeast D-amino acid oxidase, the FAD binding domain includes only the initial bab fold in a continuous segment of 30 residues, but betwee...

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Section: Introductionmentioning

confidence: 99%

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confidence: 96%

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confidence: 99%

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Proteopedia: Rossmann fold: A beta‐alpha‐beta fold at dinucleotide binding sites

Hanukoglu

2015

Biochem Molecular Bio Educ

114

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“…The core element of this conserved fold consists of seven‐stranded β‐sheets with three helices on each side, a structural feature commonly referred to as the Rossman fold 2b, 41. This core is shared among MTases that act on all different substrates, ranging from small molecules to DNA and proteins 3, 42.…”

Section: Labeling Strategies Using Adomet‐dependent Mtasesmentioning

confidence: 99%

Methyltransferase‐Directed Labeling of Biomolecules and its Applications

et al. 2017

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Methyltransferases (MTases) form a large family of enzymes that methylate a diverse set of targets, ranging from the three major biopolymers to small molecules. Most of these MTases use the cofactor S‐adenosyl‐l‐Methionine (AdoMet) as a methyl source. In recent years, there have been significant efforts toward the development of AdoMet analogues with the aim of transferring moieties other than simple methyl groups. Two major classes of AdoMet analogues currently exist: doubly‐activated molecules and aziridine based molecules, each of which employs a different approach to achieve transalkylation rather than transmethylation. In this review, we discuss the various strategies for labelling and functionalizing biomolecules using AdoMet‐dependent MTases and AdoMet analogues. We cover the synthetic routes to AdoMet analogues, their stability in biological environments and their application in transalkylation reactions. Finally, some perspectives are presented for the potential use of AdoMet analogues in biology research, (epi)genetics and nanotechnology.

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“…It is possible that an exceedingly large number of conformations may be derived from this relatively small number of secondary structure motifs if one considers the longer range arrangements of these motifs. It is known that families of protein folds exist [16][17] and it is possible that an analogous situation may exist in complex RNA which may be discerned through the comparison of tertiary structures of RNA molecules.…”

Section: Introductionmentioning

confidence: 99%

Representation, searching and discovery of patterns of bases in complex RNA structures

Harrison

South

Willett

et al. 2003

Journal of Computer-Aided Molecular Design

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SummaryWe describe a graph theoretic method designed to perform efficient searches for substructural patterns in nucleic acid structural coordinate databases using a simplified vectorial representation. Two vectors represent each nucleic acid base and the relative positions of bases with respect to one another are described in terms of distances between the defined start and end points of the vectors on each base. These points comprise the nodes and the distances the edges of a graph, and a pattern search can then be performed using a subgraph isomorphism algorithm.The minimal representation was designed to facilitate searches for complex patterns but was first tested on simple, well-characterised arrangements of bases such as base pairs and GNRA-tetraloop receptor interactions. The method performed very well for these interaction types. A survey of side-by-side base interactions, of which the adenosine platform is the best known example also locates examples of similar base rearrangements that we consider to be 2 important in structural regulation. A number of examples were found, with GU platforms being particularly prevalent. A GC platform in the RNA of the Thermus thermophilus small ribosomal subunit is in an analogous position to an adenosine platform in other species. An unusual GG platform is also observed close to one of the substrate binding sites in Haloarcula marismortui large ribosomal subunit RNA.Abbreviations PDB Protein Databank 3D three-dimensional GNRA Guanine, N = any base, R = pyrimidine base, Adenine 3

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Comparison of super-secondary structures in proteins

Cited by 851 publications

References 19 publications

Proteopedia: Rossmann fold: A beta‐alpha‐beta fold at dinucleotide binding sites

Proteopedia: Rossmann fold: A beta‐alpha‐beta fold at dinucleotide binding sites

Methyltransferase‐Directed Labeling of Biomolecules and its Applications

Representation, searching and discovery of patterns of bases in complex RNA structures

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