1mvd: Difference between revisions
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{{Theoretical_model}} | {{Theoretical_model}} | ||
< | ==IMPROVED MODEL OF A LEXA REPRESSOR DIMER BOUND TO RECA OPERATOR== | ||
<StructureSection load='1mvd' size='340' side='right'caption='[[1mvd]]' scene=''> | |||
== Structural highlights == | |||
or the | <table><tr><td colspan='2'>For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MVD FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1mvd FirstGlance], [https://www.ebi.ac.uk/pdbsum/1mvd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mvd ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
A complete three dimensional model for the LexA repressor dimer bound to the recA operator site consistent with relevant biochemical and biophysical data for the repressor was proposed from our laboratory when no crystal structure of LexA was available. Subsequently, the crystal structures of four LexA mutants Delta(1-67) S119A, S119A, G85D and Delta(1-67) quadruple mutant in the absence of operator were reported. It is examined in this paper to what extent our previous model was correct and how, using the crystal structure of the operator-free LexA dimer we can predict an improved model of LexA dimer bound to recA operator. In our improved model, the C-domain dimerization observed repeatedly in the mutant operator-free crystals is retained but the relative orientation between the two domains within a LexA molecule changes. The crystal structure of wild type LexA with or without the recA operator cannot be solved as it autocleaves itself. We argue that the 'cleavable' cleavage site region found in the crystal structures is actually the more relevant form of the region in wild-type LexA since it agrees with the value of the pre-exponential Arrhenius factor for its autocleavage, absence of various types of trans-cleavages, difficulty in modifying the catalytic serine by diisopropyl flourophosphate and lack of cleavage at Arg 81 by trypsin; hence the concept of a 'conformational switch' inferred from the crystal structures is meaningless. | |||
Improved model of a LexA repressor dimer bound to recA operator.,Chattopadhyaya R, Pal A J Biomol Struct Dyn. 2004 Apr;21(5):681-9. PMID:14769061<ref>PMID:14769061</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1mvd" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Theoretical Model]] | ||
[[Category: Large Structures]] | |||
== | |||
< | |||
[[Category: Chattopadhyaya, R]] | [[Category: Chattopadhyaya, R]] | ||
Latest revision as of 09:56, 25 August 2021
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IMPROVED MODEL OF A LEXA REPRESSOR DIMER BOUND TO RECA OPERATORIMPROVED MODEL OF A LEXA REPRESSOR DIMER BOUND TO RECA OPERATOR
Structural highlights
Publication Abstract from PubMedA complete three dimensional model for the LexA repressor dimer bound to the recA operator site consistent with relevant biochemical and biophysical data for the repressor was proposed from our laboratory when no crystal structure of LexA was available. Subsequently, the crystal structures of four LexA mutants Delta(1-67) S119A, S119A, G85D and Delta(1-67) quadruple mutant in the absence of operator were reported. It is examined in this paper to what extent our previous model was correct and how, using the crystal structure of the operator-free LexA dimer we can predict an improved model of LexA dimer bound to recA operator. In our improved model, the C-domain dimerization observed repeatedly in the mutant operator-free crystals is retained but the relative orientation between the two domains within a LexA molecule changes. The crystal structure of wild type LexA with or without the recA operator cannot be solved as it autocleaves itself. We argue that the 'cleavable' cleavage site region found in the crystal structures is actually the more relevant form of the region in wild-type LexA since it agrees with the value of the pre-exponential Arrhenius factor for its autocleavage, absence of various types of trans-cleavages, difficulty in modifying the catalytic serine by diisopropyl flourophosphate and lack of cleavage at Arg 81 by trypsin; hence the concept of a 'conformational switch' inferred from the crystal structures is meaningless. Improved model of a LexA repressor dimer bound to recA operator.,Chattopadhyaya R, Pal A J Biomol Struct Dyn. 2004 Apr;21(5):681-9. PMID:14769061[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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