Rossmann fold
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The Rossmann fold is a tertiary fold found in
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
s that bind
nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...
s, such as enzyme
cofactors Cofactor may also refer to: * Cofactor (biochemistry), a substance that needs to be present in addition to an enzyme for a certain reaction to be catalysed * A domain parameter in elliptic curve cryptography, defined as the ratio between the order ...
FAD A fad or trend is any form of collective behavior that develops within a culture, a generation or social group in which a group of people enthusiastically follow an impulse for a short period. Fads are objects or behaviors that achieve short- ...
, NAD+, and NADP+. This fold is composed of alternating
beta strand The beta sheet, (β-sheet) (also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a g ...
s and
alpha helical The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues ear ...
segments where the beta strands are hydrogen bonded to each other forming an extended
beta sheet The beta sheet, (β-sheet) (also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a g ...
and the alpha helices surround both faces of the sheet to produce a three-layered sandwich. The classical Rossmann fold contains six beta strands whereas Rossmann-like folds, sometimes referred to as Rossmannoid folds, contain only five strands. The initial beta-alpha-beta (bab) fold is the most conserved segment of the Rossmann fold. The motif is named after
Michael Rossmann Michael G. Rossmann (30 July 1930 – 14 May 2019) was a German-American physicist, microbiologist, and Hanley Distinguished Professor of Biological Sciences at Purdue University who led a team of researchers to be the first to map the structure ...
who first noticed this structural motif in the enzyme
lactate dehydrogenase Lactate dehydrogenase (LDH or LD) is an enzyme found in nearly all living cells. LDH catalyzes the conversion of lactate to pyruvate and back, as it converts NAD+ to NADH and back. A dehydrogenase is an enzyme that transfers a hydride from on ...
in 1970 and who later observed that this was a frequently occurring motif in nucleotide binding proteins. Rossmann and Rossmannoid fold proteins are extremely common. They make up 20% of proteins with known structures in the
Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cry ...
, and are found in more than 38% of
KEGG KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis i ...
metabolic pathways. The fold is extremely versatile in that it can accommodate a wide range of ligands. They can function as metabolic enzymes, DNA/RNA binding, and regulatory proteins in addition to the traditional role.


History

The Rossmann fold was first described by Dr.
Michael Rossmann Michael G. Rossmann (30 July 1930 – 14 May 2019) was a German-American physicist, microbiologist, and Hanley Distinguished Professor of Biological Sciences at Purdue University who led a team of researchers to be the first to map the structure ...
and coworkers in 1974. He was the first to deduce the structure of lactate dehydrogenase and characterized the structural motif within this enzyme which would later be called the Rossmann fold. It was subsequently found that most dehydrogenases that utilize NAD or NADP contain this same structurally conserved Rossmann fold motif. In 1989,
Israel Hanukoglu Israel Hanukoglu ( tr, İsrael Hanukoğlu) is a Turkish-born Israeli scientist. He is a full professor of biochemistry and molecular biology at Ariel University and former science and technology adviser to the prime minister of Israel (1996–199 ...
from the
Weizmann Institute of Science The Weizmann Institute of Science ( he, מכון ויצמן למדע ''Machon Vaitzman LeMada'') is a public research university in Rehovot, Israel, established in 1934, 14 years before the State of Israel. It differs from other Israeli unive ...
discovered that the consensus sequence for NADP+ binding site in some enzymes that utilize NADP+ differs from the NAD+ binding motif. This discovery was used to re-engineer coenzyme specificities of enzymes.


Structure

The Rossmann fold is composed of six parallel
beta strand The beta sheet, (β-sheet) (also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a g ...
s that form an extended
beta sheet The beta sheet, (β-sheet) (also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a g ...
. The first three strands are connected by α- helices resulting in a beta-alpha-beta-alpha-beta structure. This pattern is duplicated once to produce an inverted tandem repeat containing six strands. Overall, the strands are arranged in the order of 321456 (1 = N-terminal, 6 = C-terminal). Five stranded Rossmann-like folds are arranged in the order 32145. The overall tertiary structure of the fold resembles a three-layered sandwich wherein the filling is composed of an extended beta sheet and the two slices of bread are formed by the connecting parallel alpha-helices. One of the features of the Rossmann fold is its co-factor binding specificity. Through the analysis of four NADH-binding enzymes, it was found that in all four enzymes the nucleotide co-factor entailed the same conformation and orientation with respect to the polypeptide chain. The fold may contain additional strands joined by short helices or coils. The most conserved segment of Rossmann folds is the first beta-alpha-beta segment. Since this segment is in contact with the ADP portion of dinucleotides such as
FAD A fad or trend is any form of collective behavior that develops within a culture, a generation or social group in which a group of people enthusiastically follow an impulse for a short period. Fads are objects or behaviors that achieve short- ...
, NAD and
NADP Nicotinamide adenine dinucleotide phosphate, abbreviated NADP or, in older notation, TPN (triphosphopyridine nucleotide), is a cofactor used in anabolic reactions, such as the Calvin cycle and lipid and nucleic acid syntheses, which require N ...
it is also called as an "ADP-binding beta-beta fold.


Function

The function of the Rossmann fold in enzymes is to bind nucleotide cofactors. It also often contributes to substrate binding. Metabolic enzymes normally have one specific function, and in the case of
UDP-glucose 6-dehydrogenase UDP-glucose 6-dehydrogenase is a cytosolic enzyme that in humans is encoded by the ''UGDH'' gene. The protein encoded by this gene converts UDP-glucose to UDP-glucuronate and thereby participates in the biosynthesis of glycosaminoglycans such as ...
, the primary function is to catalyze the two step NAD(+)-dependent oxidation of
UDP-glucose Uridine diphosphate glucose (uracil-diphosphate glucose, UDP-glucose) is a nucleotide sugar. It is involved in glycosyltransferase reactions in metabolism. Functions UDP-glucose is used in nucleotide sugar metabolism as an activated form of gl ...
into
UDP-glucuronic acid UDP-glucuronic acid is a sugar used in the creation of polysaccharides and is an intermediate in the biosynthesis of ascorbic acid (except in primates and guinea pigs). It is made from UDP-glucose by UDP-glucose 6-dehydrogenase (EC 1.1.1.22) usin ...
. The N- and C-terminal domains of UgdG share structural features with ancient mitochondrial ribonucleases named MAR. MARs are present in lower eukaryotic microorganisms, have a Rossmannoid-fold and belong to the isochorismatase superfamily. This observation reinforces that the Rossmann structural motifs found in NAD(+)-dependent dehydrogenases can have a dual function working as a nucleotide cofactor binding domain and as a ribonuclease.


Evolution


Rossman and Rossmannoids

The evolutionary relationship between the Rossmann fold and Rossmann-like folds is unclear. These folds are referred to as Rossmannoids. It has been hypothesized that all these folds, including a Rossmann fold originated from a single common ancestral fold, that had nucleotide binding capabilities, in addition to non-specific catalytic activity. However, an analysis of the PDB finds evidence of
convergent evolution Convergent evolution is the independent evolution of similar features in species of different periods or epochs in time. Convergent evolution creates analogous structures that have similar form or function but were not present in the last com ...
with 156 separate H-groups of demonstrable homology, from which 123 X-groups of probable homology can be found. The groups have been integrated into
ECOD The Evolutionary Classification of Protein Domains (ECOD) is a biological database that classifies protein domains available from the Protein Data Bank. The ECOD tries to determine the evolutionary relationships between proteins. Similar to Pfam ...
.


Conventional Rossman group

Phylogenetic analysis of the NADP binding enzyme
adrenodoxin reductase Adrenodoxin reductase (Enzyme Nomenclature name: adrenodoxin-NADP+ reductase, EC 1.18.1.6), was first isolated from bovine adrenal cortex where it functions as the first enzyme in the mitochondrial P450 systems that catalyze essential steps in st ...
revealed that from prokaryotes, through metazoa and up to primates the sequence motif difference from that of most FAD and NAD-binding sites is strictly conserved. In many articles and textbooks, a Rossmann fold is defined as a strict repeated series of βαβ structure. Yet, comprehensive examination of the Rossmann folds in many NAD(P) and FAD binding sites revealed that only the first βα structure is strictly conserved. In some enzymes, there may be many loops and several helices (i.e., not a single helix) between the beta strands that form the beta-sheet. These enzymes have a common origin indicated by conserved sequence and structural features, according to Hanukoglu. The result by Hanukoglu (2017) is corroborated by Medvedev et al. (2020), in the form of an ECOD "H-group" called
Rossmann-related
. Even within this group, ECOD describes a wide range of non-nucleotide activities.


References


External links


Proteopedia page on the Rossmann folds
{{DEFAULTSORT:Rossmann Fold Protein folds Protein structural motifs