1gfx: Difference between revisions
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[[ | ==UMUD' BASED MODEL OF A LAMBDA REPRESSOR TETRAMER (TWO DIMERS) BOUND TO TWO ADJACENT OPERATOR SITES== | ||
<StructureSection load='1gfx' size='340' side='right' caption='[[1gfx]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GFX FirstGlance]. <br> | |||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gfx FirstGlance], [http://www.ebi.ac.uk/pdbsum/1gfx PDBsum]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
A model for residues 93-236 of the lambda repressor (1gfx) was predicted, based on the UmuD(') crystal structure, as part of four intact repressor molecules bound to two adjacent operator sites. The structure of region 136-230 in 1gfx was found to be nearly identical to the independently determined crystal structure of the 132-236 fragment, 1f39, released later by the PDB. Later, two more tetrameric models of the lambda repressor tetramer bound to two adjacent operator sites were constructed by us; in one of these, 1j5g, the N-domain and C-domain coordinates and hence monomer-monomer and dimer-dimer interactions are almost the same as in 1gfx, but the structure of the linker region is partly based on the linker region of the LexA dimer in 1jhe; in the other, 1lwq, the crystalline tetramer for region 140-236 has been coopted from the crystal structure deposited in 1kca, the operator DNA and N-domain coordinates of which are same as those in 1gfx and 1j5g, but the linker region is partly based on the LexA dimer structures 1jhe and 1jhh. Monomer-monomer interactions at the same operator site are stabilized by exposed hydrophobic side chains in beta-strands while cooperative interactions are mostly confined to beta(6) and some adjacent residues in both 1gfx and 1j5g. Mutational data, existence of a twofold axis relating two C-domains within a dimer, and minimization of DNA distortion between adjacent operator sites allow us to roughly position the C-domain with respect to the N-domain for both 1gfx and 1j5g. The study correlates these models with functional, biochemical, biophysical, and immunological data on the repressor in the literature. The oligomerization mode observed in the crystal structure of 132-236 may not exist in the intact repressor bound to the operator since it is shown to contradict several published biochemical data on the intact repressor. | |||
A comparative three-dimensional model of the carboxy-terminal domain of the lambda repressor and its use to build intact repressor tetramer models bound to adjacent operator sites.,Chattopadhyaya R, Ghosh K J Struct Biol. 2003 Feb;141(2):103-14. PMID:12615536<ref>PMID:12615536</ref> | |||
== | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | |||
<div class="pdbe-citations 1gfx" style="background-color:#fffaf0;"></div> | |||
== References == | |||
== | <references/> | ||
< | __TOC__ | ||
</StructureSection> | |||
[[Category: Theoretical Model]] | |||
[[Category: Chattopadhyaya, R]] | [[Category: Chattopadhyaya, R]] | ||
[[Category: Ghosh, K]] | [[Category: Ghosh, K]] | ||
Latest revision as of 11:58, 11 February 2016
 |
UMUD' BASED MODEL OF A LAMBDA REPRESSOR TETRAMER (TWO DIMERS) BOUND TO TWO ADJACENT OPERATOR SITESUMUD' BASED MODEL OF A LAMBDA REPRESSOR TETRAMER (TWO DIMERS) BOUND TO TWO ADJACENT OPERATOR SITES
Structural highlights
Publication Abstract from PubMedA model for residues 93-236 of the lambda repressor (1gfx) was predicted, based on the UmuD(') crystal structure, as part of four intact repressor molecules bound to two adjacent operator sites. The structure of region 136-230 in 1gfx was found to be nearly identical to the independently determined crystal structure of the 132-236 fragment, 1f39, released later by the PDB. Later, two more tetrameric models of the lambda repressor tetramer bound to two adjacent operator sites were constructed by us; in one of these, 1j5g, the N-domain and C-domain coordinates and hence monomer-monomer and dimer-dimer interactions are almost the same as in 1gfx, but the structure of the linker region is partly based on the linker region of the LexA dimer in 1jhe; in the other, 1lwq, the crystalline tetramer for region 140-236 has been coopted from the crystal structure deposited in 1kca, the operator DNA and N-domain coordinates of which are same as those in 1gfx and 1j5g, but the linker region is partly based on the LexA dimer structures 1jhe and 1jhh. Monomer-monomer interactions at the same operator site are stabilized by exposed hydrophobic side chains in beta-strands while cooperative interactions are mostly confined to beta(6) and some adjacent residues in both 1gfx and 1j5g. Mutational data, existence of a twofold axis relating two C-domains within a dimer, and minimization of DNA distortion between adjacent operator sites allow us to roughly position the C-domain with respect to the N-domain for both 1gfx and 1j5g. The study correlates these models with functional, biochemical, biophysical, and immunological data on the repressor in the literature. The oligomerization mode observed in the crystal structure of 132-236 may not exist in the intact repressor bound to the operator since it is shown to contradict several published biochemical data on the intact repressor. A comparative three-dimensional model of the carboxy-terminal domain of the lambda repressor and its use to build intact repressor tetramer models bound to adjacent operator sites.,Chattopadhyaya R, Ghosh K J Struct Biol. 2003 Feb;141(2):103-14. PMID:12615536[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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