Structural templates: Difference between revisions

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==Motifs In Proteins==

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

<OL>

<LI>A particular amino-acid sequence that characterises a biochemical function

<LI>A set of secondary structure elements that defines a functional or structural role

</OL>

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 '''[http://www.ebi.ac.uk/interpro/IEntry?ac=IPR007087 zinc finger motif]''' which is readily identified from the following consensus sequence pattern (where "X" represents ''any'' amino acid):

'''Cys''' - X(2-4) - '''Cys''' - X(3) - Phe - X(5) - Leu - X(2) - '''His''' - X(3) - '''His'''

The example structure shown to <scene name='40/401510/Cv/3'>illustrate the motif</scene> is that of Zif268 protein-DNA complex from Mus musculus (PDB entry 1AAY). In this example (a C2H2 class zinc finger) the conserved <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_cysteine/1'>cysteine</scene> and <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_histidine/2'>histidine</scene> residues form ligands to a <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_zn/1'>zinc ion</scene> whose coordination is essential to stabilise the tertiary fold of the protein. The fold is important because it helps orientate the <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_recognition/1'>recognition helices</scene> to bind to the <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_major_groove/1'>major groove of the DNA</scene>.

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@@ Line 1: / Line 1: @@
 <StructureSection load='1aay' size='350' side='right' caption='Caption for this structure' scene=''>
+==Motifs In Proteins==
+The term "motif" when used in structural biology tends to refer to one of two cases:
+<OL>
+<LI>A particular amino-acid sequence that characterises a biochemical function
+<LI>A set of secondary structure elements that defines a functional or structural role
+</OL>
+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 '''[http://www.ebi.ac.uk/interpro/IEntry?ac=IPR007087 zinc finger motif]''' which is readily identified from the following consensus sequence pattern (where "X" represents ''any'' amino acid):<br/>
+'''Cys''' - X<sub>(2-4)</sub> - '''Cys''' - X<sub>(3)</sub> - Phe - X<sub>(5)</sub> - Leu - X<sub>(2)</sub> - '''His''' - X<sub>(3)</sub> - '''His''' <br/>
+<br/>
 The example structure shown to <scene name='40/401510/Cv/3'>illustrate the motif</scene> is that of Zif268 protein-DNA complex from Mus musculus (PDB entry 1AAY). In this example (a C2H2 class zinc finger) the conserved <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_cysteine/1'>cysteine</scene> and <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_histidine/2'>histidine</scene> residues form ligands to a <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_zn/1'>zinc ion</scene> whose coordination is essential to stabilise the tertiary fold of the protein. The fold is important because it helps orientate the <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_recognition/1'>recognition helices</scene> to bind to the <scene name='User:James_D_Watson/Structural_Templates/Zinc_finger_major_groove/1'>major groove of the DNA</scene>.