Sand box 211: Difference between revisions

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<scene name='Sand_box_211/1exn/4'>T5 5'-exonuclease</scene> is a homodimeric protein composed of two identical chains,<scene name='Sand_box_211/Vghjvjh/4'>chain a</scene> and <scene name='Sand_box_211/Vhj/3'>chain b</scene>.

Both chains contain a hole, bound by a <scene name='Celina_Pinto/Sandbox_211/Helical_arch/2'>helical arch</scene> composed of two helices in which hydrophobic and positively charged residues are located. The helical arch is situated in front of the active site and only single-stranded DNA can pass through it. Since the enzyme is able to cleave double-stranded DNA, the enzyme has a conformational flexibility to facilitate DNA threading which is required to process the 5' nuclease substrates in the active site.

Both chains contain a hole, bound by a <scene name='Celina_Pinto/Sandbox_211/Helical_arch/2'>helical arch</scene> composed of two helices in which <scene name='Celina_Pinto/Sandbox_211/Residues_helical_arch/2'>hydrophobic and positively charged residues</scene> are located. The helical arch is situated in front of the active site and only single-stranded DNA can pass through it. Since the enzyme is able to cleave double-stranded DNA, the enzyme has a conformational flexibility to facilitate DNA threading which is required to process the 5' nuclease substrates in the active site.

The core regions of the enzyme are composed of beta-sheets and alpha-helices . These form the base of the active site pocket which bind the catalytic metal ions.

The core regions of the enzyme are composed of <scene name='Celina_Pinto/Sandbox_211/Helix_sheet/1'>beta-sheets and alpha-helices</scene>. These form the base of the active site pocket which bind the catalytic metal ions.

The active site possesses 8 conserved <scene name='Sand_box_211/8_residus/3'>acidic residues</scene> (Asp26, Asp68, Glu128, Asp130, Asp153, Asp155, Asp201, Asp204) which interact with divalent metal ions. <scene name='Sand_box_211/Try82/2'>Tyr82</scene> is also a conserved residue located in the active site, but it doesn't seem to have an important role since its mutation doesn't dramatically change the affinity to bind DNA.

Sand box 211: Difference between revisions

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 <Structure load='1EXN' size='500' frame='true' align='right' caption='T5 5'exonuclease' scene='Insert optional scene name here' />
 <scene name='Sand_box_211/1exn/4'>T5 5'-exonuclease</scene> is a homodimeric protein composed of two identical chains,<scene name='Sand_box_211/Vghjvjh/4'>chain a</scene> and <scene name='Sand_box_211/Vhj/3'>chain b</scene>.
-Both chains contain a hole, bound by a  <scene name='Celina_Pinto/Sandbox_211/Helical_arch/2'>helical arch</scene> composed of two helices in which hydrophobic and positively charged residues are located. The helical arch is situated in front of the active site and only single-stranded DNA can pass through it. Since the enzyme is able to cleave double-stranded DNA, the enzyme has a conformational flexibility to facilitate DNA threading which is required to process the 5' nuclease substrates in the active site.
+Both chains contain a hole, bound by a  <scene name='Celina_Pinto/Sandbox_211/Helical_arch/2'>helical arch</scene> composed of two helices in which <scene name='Celina_Pinto/Sandbox_211/Residues_helical_arch/2'>hydrophobic and positively charged residues</scene> are located. The helical arch is situated in front of the active site and only single-stranded DNA can pass through it. Since the enzyme is able to cleave double-stranded DNA, the enzyme has a conformational flexibility to facilitate DNA threading which is required to process the 5' nuclease substrates in the active site.
-The core regions of the enzyme are composed of beta-sheets and alpha-helices . These form the base of the active site pocket which bind the catalytic metal ions.
+The core regions of the enzyme are composed of <scene name='Celina_Pinto/Sandbox_211/Helix_sheet/1'>beta-sheets and alpha-helices</scene>. These form the base of the active site pocket which bind the catalytic metal ions.
 The active site possesses 8 conserved <scene name='Sand_box_211/8_residus/3'>acidic residues</scene> (Asp26, Asp68, Glu128, Asp130, Asp153, Asp155, Asp201, Asp204) which interact with divalent metal ions. <scene name='Sand_box_211/Try82/2'>Tyr82</scene> is also a conserved residue located in the active site, but it doesn't seem to have an important role since its mutation doesn't dramatically change the affinity to bind DNA.