1per: Difference between revisions

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[[Image:1per.gif|left|200px]]<br />

[[Image:1per.gif|left|200px]]<br /><applet load="1per" size="350" color="white" frame="true" align="right" spinBox="true"

<applet load="1per" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

caption="1per, resolution 2.500Å" />

'''THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES'''<br />

==Overview==

BACKGROUND: The repressor of phage 434 binds to a set of operator sites as, a homodimer. Its relative affinities for these sites determine the switch, from lysogenic to lytic growth. The six 434 operator sites (OR1, OR2, OR3, OL1, OL2 and OL3) have a particularly simple organization; all are 14 base, pairs long, with a conserved 5'-ACAA sequence symmetrically placed at, either end, and a variable central six base pairs. OR3 is unique among, naturally-occurring 434 operator sites in that it contains a non-consensus, base pair, G.C, at the fourth position of the otherwise invariant 5'-ACAA, sequence. Comparisons among structures of the 434 repressor DNA-binding, domain, R1-69, bound to various operator sites, allow us to analyze, differential specificity in regulatory complexes of this kind. RESULTS: We, have determined the structure at 2.5 A resolution of a complex of R1-69, with DNA containing the OR3 site and compared it with previously studied, complexes of R1-69 bound to OR1 and OR2. There are surprisingly extensive, structural differences between the consensus and non-consensus half-sites, of OR3 with respect to their interactions with R1-69, including a shift in, the DNA backbone and a small rotation of the entire R1-69 monomer., CONCLUSIONS: Recognition of the base pair difference that is critical for, the 434 regulatory switch involves a number of amino acid residues, not, just the one or two side chains in direct contact with the G-C base pair., Moreover, the repressor imposes a somewhat altered DNA conformation on the, non-consensus half-site.

BACKGROUND: The repressor of phage 434 binds to a set of operator sites as a homodimer. Its relative affinities for these sites determine the switch from lysogenic to lytic growth. The six 434 operator sites (OR1, OR2, OR3, OL1, OL2 and OL3) have a particularly simple organization; all are 14 base pairs long, with a conserved 5'-ACAA sequence symmetrically placed at either end, and a variable central six base pairs. OR3 is unique among naturally-occurring 434 operator sites in that it contains a non-consensus base pair, G.C, at the fourth position of the otherwise invariant 5'-ACAA sequence. Comparisons among structures of the 434 repressor DNA-binding domain, R1-69, bound to various operator sites, allow us to analyze differential specificity in regulatory complexes of this kind. RESULTS: We have determined the structure at 2.5 A resolution of a complex of R1-69 with DNA containing the OR3 site and compared it with previously studied complexes of R1-69 bound to OR1 and OR2. There are surprisingly extensive structural differences between the consensus and non-consensus half-sites of OR3 with respect to their interactions with R1-69, including a shift in the DNA backbone and a small rotation of the entire R1-69 monomer. CONCLUSIONS: Recognition of the base pair difference that is critical for the 434 regulatory switch involves a number of amino acid residues, not just the one or two side chains in direct contact with the G-C base pair. Moreover, the repressor imposes a somewhat altered DNA conformation on the non-consensus half-site.

==About this Structure==

1PER is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_434 Bacteriophage 434]. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA].

1PER is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_434 Bacteriophage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA].

==Reference==

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Line 13:

[[Category: Bacteriophage 434]]

[[Category: Single protein]]

[[Category: Harrison, S.C.]]

[[Category: Harrison, S C.]]

[[Category: Rodgers, D.W.]]

[[Category: Rodgers, D W.]]

[[Category: protein-dna complex]]

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@@ Line 1: / Line 1: @@
-[[Image:1per.gif|left|200px]]<br />
+[[Image:1per.gif|left|200px]]<br /><applet load="1per" size="350" color="white" frame="true" align="right" spinBox="true"
-<applet load="1per" size="450" color="white" frame="true" align="right" spinBox="true"
 caption="1per, resolution 2.500&Aring;" />
 '''THE COMPLEX BETWEEN PHAGE 434 REPRESSION DNA-BINDING DOMAIN AND OPERATOR SITE OR3: STRUCTURAL DIFFERENCES BETWEEN CONSENSUS AND NON-CONSENSUS HALF-SITES'''<br />
 ==Overview==
-BACKGROUND: The repressor of phage 434 binds to a set of operator sites as, a homodimer. Its relative affinities for these sites determine the switch, from lysogenic to lytic growth. The six 434 operator sites (OR1, OR2, OR3, OL1, OL2 and OL3) have a particularly simple organization; all are 14 base, pairs long, with a conserved 5'-ACAA sequence symmetrically placed at, either end, and a variable central six base pairs. OR3 is unique among, naturally-occurring 434 operator sites in that it contains a non-consensus, base pair, G.C, at the fourth position of the otherwise invariant 5'-ACAA, sequence. Comparisons among structures of the 434 repressor DNA-binding, domain, R1-69, bound to various operator sites, allow us to analyze, differential specificity in regulatory complexes of this kind. RESULTS: We, have determined the structure at 2.5 A resolution of a complex of R1-69, with DNA containing the OR3 site and compared it with previously studied, complexes of R1-69 bound to OR1 and OR2. There are surprisingly extensive, structural differences between the consensus and non-consensus half-sites, of OR3 with respect to their interactions with R1-69, including a shift in, the DNA backbone and a small rotation of the entire R1-69 monomer., CONCLUSIONS: Recognition of the base pair difference that is critical for, the 434 regulatory switch involves a number of amino acid residues, not, just the one or two side chains in direct contact with the G-C base pair., Moreover, the repressor imposes a somewhat altered DNA conformation on the, non-consensus half-site.
+BACKGROUND: The repressor of phage 434 binds to a set of operator sites as a homodimer. Its relative affinities for these sites determine the switch from lysogenic to lytic growth. The six 434 operator sites (OR1, OR2, OR3, OL1, OL2 and OL3) have a particularly simple organization; all are 14 base pairs long, with a conserved 5'-ACAA sequence symmetrically placed at either end, and a variable central six base pairs. OR3 is unique among naturally-occurring 434 operator sites in that it contains a non-consensus base pair, G.C, at the fourth position of the otherwise invariant 5'-ACAA sequence. Comparisons among structures of the 434 repressor DNA-binding domain, R1-69, bound to various operator sites, allow us to analyze differential specificity in regulatory complexes of this kind. RESULTS: We have determined the structure at 2.5 A resolution of a complex of R1-69 with DNA containing the OR3 site and compared it with previously studied complexes of R1-69 bound to OR1 and OR2. There are surprisingly extensive structural differences between the consensus and non-consensus half-sites of OR3 with respect to their interactions with R1-69, including a shift in the DNA backbone and a small rotation of the entire R1-69 monomer. CONCLUSIONS: Recognition of the base pair difference that is critical for the 434 regulatory switch involves a number of amino acid residues, not just the one or two side chains in direct contact with the G-C base pair. Moreover, the repressor imposes a somewhat altered DNA conformation on the non-consensus half-site.
 ==About this Structure==
-PER is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_434 Bacteriophage 434]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA].
+PER is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_434 Bacteriophage 434]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PER OCA].
 ==Reference==
@@ Line 14: / Line 13: @@
 [[Category: Bacteriophage 434]]
 [[Category: Single protein]]
-[[Category: Harrison, S.C.]]
+[[Category: Harrison, S C.]]
-[[Category: Rodgers, D.W.]]
+[[Category: Rodgers, D W.]]
 [[Category: protein-dna complex]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Thu Nov  8 12:41:47 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:28:02 2008''