Sand box 211: Difference between revisions
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== '''Structure''' == | == '''Structure''' == | ||
<Structure load='1EXN' size='500' frame='true' align='right' caption=' | <Structure load='1EXN' size='500' frame='true' align='right' caption='T5 5'exonuclease' scene='Insert optional scene name here' /> | ||
T5 5'-exonuclease is a homodimer composed of two identical chains,<scene name='Sand_box_211/Hghg/1'>chain a</scene><scene name='Sand_box_211/Vfsvcvvf/1'>TextToBeDisplayed</scene> and <scene name='Sand_box_211/Fhh/1'>chain b</scene><scene name='Sand_box_211/Cvvv/1'>TextToBeDisplayed</scene>. Both chains contain a hole, bound by a helical arch composed of two helices<scene name='Sand_box_211/Helice_alpha/1'>TextToBeDisplayed</scene> in which hydrophobic<scene name='Sand_box_211/Hydrophobe/1'>TextToBeDisplayed</scene> and positively charged residues<scene name='Sand_box_211/Residus_plus/2'>TextToBeDisplayed</scene><scene name='Sand_box_211/Residus_plus/3'>TextToBeDisplayed</scene> <scene name='Sand_box_211/Hydrophobe_et_plus/1'>TextToBeDisplayed</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 helical arch may be able to change conformation in order to free the active site. | |||
T5 5'-exonuclease is a homodimer composed of two identical chains, chain a and chain b. Both chains contain a hole, bound by a helical arch 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 helical arch may be able to change conformation in order to free the active site. | |||
The active site possesses 8 conserved acidic residues (Asp26, Asp68, Glu128, Asp130, Asp153, Asp155, Asp201, Asp204) which interact with divalent metal ions. Tyr82 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. | The active site possesses 8 conserved acidic residues (Asp26, Asp68, Glu128, Asp130, Asp153, Asp155, Asp201, Asp204) which interact with divalent metal ions. Tyr82 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. | ||
Six residues (Arg33, Lys83, Arg172, Lys 196, Lys215, Arg216 and Lys241) near the active site permit binding to branched DNA. | Six residues (Arg33, Lys83, Arg172, Lys 196, Lys215, Arg216 and Lys241) near the active site permit binding to branched DNA. | ||
