Rossmann fold: Difference between revisions
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Note: This entry on the Rossmann fold has been published in Biochem. Mol. Biol. Educ.<ref name="Hanukoglu-2015">PMID:25704928</ref>. Please cite it as Biochem. Mol. Biol. Educ. 43:206-209, 2015. | |||
The Rossmann fold is a super-secondary structure that is characterized by an alternating motif of beta-strand-alpha helix-beta strand secondary structures. Hence this fold is also called a βαβ fold. The β-strands participate in the formation of a β-sheet. The βαβ fold structure is commonly observed in enzymes that have dinucleotide coenzymes, such as FAD, NAD and NADP. | The Rossmann fold is a super-secondary structure that is characterized by an alternating motif of beta-strand-alpha helix-beta strand secondary structures. Hence this fold is also called a βαβ fold. The β-strands participate in the formation of a β-sheet. The βαβ fold structure is commonly observed in enzymes that have dinucleotide coenzymes, such as FAD, NAD and NADP. | ||
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In dinucleotide binding flavoproteins, FAD binding Rossmann fold is commonly located close to the amino terminus of the protein. Figure 2 shows the first Rossmann fold of two flavoproteins, D-amino acid oxidase ([[2e48]])<ref>PMID:17303072</ref> and glutathione reductase ([[3grs]])<ref>PMID:3656429</ref>. In both enzymes, the first β-strand is followed by a tight loop that is connected to the N-terminal of the helix. The two highly conserved Gly residues in the consensus sequence are located in this turn to allow the sharp bending of the chain. At the end of the helix there is a wider turn that is followed by the second beta strand that runs parallel to the first strand. | In dinucleotide binding flavoproteins, FAD binding Rossmann fold is commonly located close to the amino terminus of the protein. Figure 2 shows the first Rossmann fold of two flavoproteins, D-amino acid oxidase ([[2e48]])<ref>PMID:17303072</ref> and glutathione reductase ([[3grs]])<ref>PMID:3656429</ref>. In both enzymes, the first β-strand is followed by a tight loop that is connected to the N-terminal of the helix. The two highly conserved Gly residues in the consensus sequence are located in this turn to allow the sharp bending of the chain. At the end of the helix there is a wider turn that is followed by the second beta strand that runs parallel to the first strand. | ||
The FAD structure is shown in CPK format. The atoms can be identified by their colors: <span style="color:Gray">Carbon</span>; <span style="color:red">Oxygen</span>, <span style="color:DarkOrange">Phosphorus</span> and <span style="color:SlateBlue">Nitrogen</span>. The turn at β-α border is in contact with the negatively charged <span style="color:red">oxygens</span> of the two <span style="color:DarkOrange">phosphate</span> groups. | The FAD structure is shown in CPK format. The atoms can be identified by their colors: <span style="color:Gray">Carbon</span>; <span style="color:red">Oxygen</span>, <span style="color:DarkOrange">Phosphorus</span> and <span style="color:SlateBlue">Nitrogen</span>. The turn at the β-α border is in contact with the negatively charged <span style="color:red">oxygens</span> of the two <span style="color:DarkOrange">phosphate</span> groups. | ||
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The following scenes illustrate some aspects of the structure. | The following scenes illustrate some aspects of the structure. | ||
As noted above, the Rossmann fold is associated with a specific consensus sequence of Gly-x-Gly-x-x-Gly at the region of the tight loop between the first β-strand the α-helix. | |||
The first two scenes demonstrate the location of the first two conserved glycines. | |||
To rotate the molecule click and hold left mouse button. | To rotate the molecule click and hold left mouse button. | ||
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[[Image:3-phosphoglycerate_dehydrogenase-2P9E-sheet.png|400px|right|thumb| Fig. 5. 3-phosphoglycerate dehydrogenase ([[2p9e]]) beta sheet in the NAD binding domain. The two beta-strands that form the core of the Rossmann fold are marked in dark-blue ( <span style="color:MediumBlue">██</span> )color.]] | [[Image:3-phosphoglycerate_dehydrogenase-2P9E-sheet.png|400px|right|thumb| Fig. 5. 3-phosphoglycerate dehydrogenase ([[2p9e]]) beta sheet in the NAD binding domain. The two beta-strands that form the core of the Rossmann fold are marked in dark-blue ( <span style="color:MediumBlue">██</span> )color.]] | ||
As seen in the above example of ferredoxin reductase the β-sheet that is in the nucleotide domain may have more than two strands. In many (but not all) proteins with βαβ fold, the β-strands may be part of a larger β-sheet with up to seven β-strands. Figure 5 shows five strands forming a β-sheet in phosphoglycerate dehydrogenase ([[2p9e]]). Note that the segment connecting the second strand to the third is in coiled confirmation and not helical. Whereas the subsequent connections between strands include α-helix segments. | As seen in the above example of ferredoxin reductase the β-sheet that is in the nucleotide domain may have more than two strands. In many (but not all) proteins with βαβ fold, the β-strands may be part of a larger β-sheet with up to seven β-strands. Figure 5 shows five strands forming a β-sheet in phosphoglycerate dehydrogenase ([[2p9e]]). Note that the segment connecting the second strand to the third is in coiled confirmation and not helical. Whereas the subsequent connections between strands include α-helix segments. | ||
As seen in the example in Fig. 5, the direction of the strands are all parallel. This represents a general trend in Rossmann folds. However in some Rossmann folds there may be some strands in anti-parallel direction.<ref name="Hanukoglu-2015" /> | |||
As compared to the direction of the β-strands, the direction of the helical segments is generally anti-parallel to the β-strands (Fig. 5). | |||
In some Rossmann fold domains, the segments in between the β-strands may include a complex series of helical and coiled segments (for example see [[3bhi]]). | |||
==Evolutionary origin of the βαβ fold == | ==Evolutionary origin of the βαβ fold == | ||
A myriad of proteins include the βαβ Rossmann fold. Many of these proteins can be grouped in a hierarchy of families based on their sequence similarities <ref>PMID:11514662</ref>,<ref>PMID:8749365</ref>,<ref>PMID:17658942</ref>. Yet, many of these families do not show any significant sequence homology across families. | A myriad of proteins include the βαβ Rossmann fold. Proteopedia includes a list of over 1,000 PDB structures with [[:Category:Rossmann fold | Rossmann fold]]. Many of these proteins can be grouped in a hierarchy of families based on their sequence similarities <ref>PMID:11514662</ref>,<ref>PMID:8749365</ref>,<ref>PMID:17658942</ref>. Yet, many of these families do not show any significant sequence homology across families. | ||
The observation that the βαβ structure and its consensus sequence is observed in many seemingly unrelated proteins raises the question whether the origin of the βαβ fold of all these proteins is a common ancestral sequence. Alternatively, there is also a possibility that this structure emerged in different proteins independently. | The observation that the βαβ structure and its consensus sequence is observed in many seemingly unrelated proteins raises the question whether the origin of the βαβ fold of all these proteins is a common ancestral sequence. Alternatively, there is also a possibility that this structure emerged in different proteins independently. | ||
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[[Category:Topic Page]] | [[Category:Topic Page]] | ||
[[Category: Rossmann fold]] | [[Category: Rossmann fold]] | ||
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