User:James D Watson/Structural Templates: Difference between revisions

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==Nests==

Smaller than loops and turns are some recently discovered motifs known as "nests". These are mainchain conformations where 3 successive amide groups form a positively charged concavity capable of binding one or more negatively charged atoms (Figure 1). They are characterised by alternating enantiomeric mainchain dihedral angles from the alpha and gamma regions of the Ramachandran plot, and can be of RL (right handed - left handed) or LR type. They are most commonly found as part of previously described hydrogen bonded structural motifs but are also found at functional sites.<br>

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In compound nests the result is a long chain with all the overlapping nests facing a similar direction. This basically forms a much wider nest that is capable of binding a larger anionic group of atoms such as the phosphate ion, and are usually functionally important motifs. Tandem nests are not as common and, due to the greater change in the direction that adjacent nests face, only seem to perform functional roles when found in conjunction with one or more compound nests.

One of the most well known functional compound nests is found in the phosphate-binding loop of Ras protein (PDB entry 5p21). The P-loop is a well described ATP- or GTP-binding loop present in a large superfamily of important proteins which includes G-proteins and kinases. The main feature of the P-loop is a long compound LRLR nest that forms a binding site for the β-phosphate of ATP or GTP. However, this is an example of a motif where the ligand also binds to the free main chain NH groups at the N-terminus of an alpha helix. On closer inspection it becomes evident that this interaction is in addition to the compound nest and does not interfere with it. Therefore the P-loop is actually more accurately described as a compound LRLR nest and an adjacent helical N-terminus that collectively bind to the α- and β-phosphates of the GDP substrate. The P-loop, which is retained throughout the superfamily, has a highly conserved GxxxxGKS/T consensus sequence (where the xxGK section forms the LRLR compound nest).

One of the most well known functional compound nests is found in the phosphate-binding loop of Ras protein (PDB entry 5p21). The <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_ploop/1'>P-loop</scene> is a well described ATP- or GTP-binding loop present in a large superfamily of important proteins which includes G-proteins and kinases. The main feature of the P-loop is a long compound LRLR nest that <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_ploop_nest/1'>forms a binding site for the β-phosphate of ATP or GTP</scene>. However, this is an example of a motif where the ligand also binds to the free main chain NH groups at the N-terminus of an alpha helix. On closer inspection it becomes evident that this interaction is in addition to the compound nest and does not interfere with it. Therefore the P-loop is actually more accurately described as a compound LRLR nest and an adjacent helical N-terminus that collectively bind to the α- and β-phosphates of the GDP substrate. The P-loop, which is retained throughout the superfamily, has a highly conserved GxxxxGKS/T consensus sequence (where the xxGK section forms the LRLR compound nest).

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 ==Nests==
 Smaller than loops and turns are some recently discovered motifs known as "nests". These are mainchain conformations where 3 successive amide groups form a positively charged concavity capable of binding one or more negatively charged atoms (Figure 1). They are characterised by alternating enantiomeric mainchain dihedral angles from the alpha and gamma regions of the Ramachandran plot, and can be of RL (right handed - left handed) or LR type. They are most commonly found as part of previously described hydrogen bonded structural motifs but are also found at functional sites.<br>
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 In compound nests the result is a long chain with all the overlapping nests facing a similar direction.  This basically forms a much wider nest that is capable of binding a larger anionic group of atoms such as the phosphate ion, and are usually functionally important motifs. Tandem nests are not as common and, due to the greater change in the direction that adjacent nests face, only seem to perform functional roles when found in conjunction with one or more compound nests.
-One of the most well known functional compound nests is found in the phosphate-binding loop of Ras protein (PDB entry 5p21). The P-loop is a well described ATP- or GTP-binding loop present in a large superfamily of important proteins which includes G-proteins and kinases. The main feature of the P-loop is a long compound LRLR nest that forms a binding site for the β-phosphate of ATP or GTP. However, this is an example of a motif where the ligand also binds to the free main chain NH groups at the N-terminus of an alpha helix. On closer inspection it becomes evident that this interaction is in addition to the compound nest and does not interfere with it. Therefore the P-loop is actually more accurately described as a compound LRLR nest and an adjacent helical N-terminus that collectively bind to the α- and β-phosphates of the GDP substrate. The P-loop, which is retained throughout the superfamily, has a highly conserved GxxxxGKS/T consensus sequence (where the xxGK section forms the LRLR compound nest).
+<applet load='1lmb' size='300' frame='true' align='left' caption='Nest in PDB entry 5p21' scene='User:James_D_Watson/Structural_Templates/Secondary_structure_start/4'/>
+One of the most well known functional compound nests is found in the phosphate-binding loop of Ras protein (PDB entry 5p21). The <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_ploop/1'>P-loop</scene> is a well described ATP- or GTP-binding loop present in a large superfamily of important proteins which includes G-proteins and kinases. The main feature of the P-loop is a long compound LRLR nest that <scene name='User:James_D_Watson/Structural_Templates/Secondary_structure_ploop_nest/1'>forms a binding site for the β-phosphate of ATP or GTP</scene>. However, this is an example of a motif where the ligand also binds to the free main chain NH groups at the N-terminus of an alpha helix. On closer inspection it becomes evident that this interaction is in addition to the compound nest and does not interfere with it. Therefore the P-loop is actually more accurately described as a compound LRLR nest and an adjacent helical N-terminus that collectively bind to the α- and β-phosphates of the GDP substrate. The P-loop, which is retained throughout the superfamily, has a highly conserved GxxxxGKS/T consensus sequence (where the xxGK section forms the LRLR compound nest).
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