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

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~~''''''Bold text''''''~~==~~Structural~~ Motifs In Proteins==

==Motifs In Proteins==

There are a great number of protein sequence motifs ~~which have been found~~, many of which have a ~~functional role~~. However, there are also a number of repeated patterns and functional motifs revealed when the protein structure is examined. This page aims to introduce ~~various~~ types of motif ~~and illustrate~~ them ~~using~~ the ~~green links in the text~~.

The term "motif" when used in structural biology tends to refer to one of two cases:

1. A particular amino-acid sequence that characterises a biochemical function

2. A set of secondary structure elements that defines a functional or structural role

There are a great number of protein sequence motifs identified, many of which have well defined structural or functional roles. One such example of this is the so-called '''zinc finger motif''' which is readily identified from the following consensus sequence pattern (where "X" represents ''any'' amino acid):

Cys-X2-4-Cys-X3-Phe-X5-Leu-X2-His-X3-His

The example structure shown to illustrate the motif is that of Zif268 protein-DNA complex from Mus musculus (PDB entry 1AAY). In this example (a C2H2 class zinc finger) the conserved cysteine and histidine residues form ligands to a zinc ion whose coordination is essential to stabilise the tertiary fold of the protein. The fold is important because it helps orientate the recogniton helices to bind to the DNA.

However, there are also a number of repeated patterns and functional motifs revealed when the protein structure is examined. This page aims to introduce some of the main types of motif illustrating them on protein structures from the PDB.

==Secondary structure elements==

~~==Global fold==~~

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-''''''Bold text''''''==Structural Motifs In Proteins==
+==Motifs In Proteins==
-There are a great number of protein sequence motifs which have been found, many of which have a functional role. However, there are also a number of repeated patterns and functional motifs revealed when the protein structure is examined. This page aims to introduce various types of motif and illustrate them using the green links in the text.
+The term "motif" when used in structural biology tends to refer to one of two cases:
+. A particular amino-acid sequence that characterises a biochemical function
+. A set of secondary structure elements that defines a functional or structural role
+There are a great number of protein sequence motifs identified, many of which have well defined structural or functional roles. One such example of this is the so-called '''zinc finger motif''' which is readily identified from the following consensus sequence pattern (where "X" represents ''any'' amino acid):
+Cys-X2-4-Cys-X3-Phe-X5-Leu-X2-His-X3-His
+The example structure shown to illustrate the motif is that of Zif268 protein-DNA complex from Mus musculus (PDB entry 1AAY). In this example (a C2H2 class zinc finger) the conserved cysteine and histidine residues form ligands to a zinc ion whose coordination is essential to stabilise the tertiary fold of the protein. The fold is important because it helps orientate the recogniton helices to bind to the DNA.
+{{STRUCTURE_1aay|  PDB=1aay  |  SCENE=  }}
+However, there are also a number of repeated patterns and functional motifs revealed when the protein structure is examined. This page aims to introduce some of the main types of motif illustrating them on protein structures from the PDB.
+==Secondary structure elements==
-==Global fold==
 {{STRUCTURE_5p21 |  PDB=5p21  |  SCENE=  }}