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1rcs

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[[Image:1rcs.gif|left|200px]]
[[Image:1rcs.gif|left|200px]]
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{{Structure
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|PDB= 1rcs |SIZE=350|CAPTION= <scene name='initialview01'>1rcs</scene>
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The line below this paragraph, containing "STRUCTURE_1rcs", creates the "Structure Box" on the page.
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene>
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{{STRUCTURE_1rcs| PDB=1rcs | SCENE= }}
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rcs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rcs OCA], [http://www.ebi.ac.uk/pdbsum/1rcs PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rcs RCSB]</span>
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'''NMR STUDY OF TRP REPRESSOR-OPERATOR DNA COMPLEX'''
'''NMR STUDY OF TRP REPRESSOR-OPERATOR DNA COMPLEX'''
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[[Category: Zhao, D.]]
[[Category: Zhao, D.]]
[[Category: Zheng, Z.]]
[[Category: Zheng, Z.]]
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[[Category: dna]]
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[[Category: Dna]]
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[[Category: dna-binding]]
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[[Category: Dna-binding]]
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[[Category: peptide]]
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[[Category: Peptide]]
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[[Category: repressor]]
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[[Category: Repressor]]
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[[Category: transcription regulation]]
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[[Category: Transcription regulation]]
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[[Category: trp]]
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[[Category: Trp]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 07:20:33 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:26:18 2008''
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Revision as of 04:20, 3 May 2008

Image:1rcs.gif

Template:STRUCTURE 1rcs

NMR STUDY OF TRP REPRESSOR-OPERATOR DNA COMPLEX


Overview

The solution structures of the complex between Escherichia coli trp holorepressor and a 20 base-pair consensus operator DNA were determined. The majority of proton chemical shifts of the trp holorepressor and operator DNA were assigned from homonuclear 2D NOESY spectra of selectively deuterated analog-operator DNA complexes and the 3D NOESY-HMQC spectrum of a uniformly 15N-labeled repressor-operator DNA complex. The structures were calculated using restrained molecular dynamics and sequential simulated annealing with 4086 NOE and other experimental constraints. The root-mean-squared deviation (RMSD) among the calculated structures and their mean is 0.9(+/- 0.3)A for the repressor backbone, 1.1(+/- 0.5)A for the DNA backbone, and 1.3(+/- 0.3)A for all heavy atoms. The DNA is deformed to a significant extent from the standard B DNA structure to fit the helix-turn-helix (HTH) segment of the repressor (helices D and E) into its major grooves. Little change is found in the ABCF core of the repressor on complexation in comparison to the free repressor, but changes in the cofactor L-tryptophan binding pocket and the HTH segment are observed. The N-terminal residues (2 to 17) are found to be disordered and do not form stable interactions with DNA. Direct H-bonding to the bases of the operator DNA is consistent with all of our observed NOE constraints. Hydrogen bonds from NH eta 1 and NH eta 2 of Arg69 to O-6 and N-7 of G2 are compatible with the solution structure, as they are with the crystal structure. Other direct H-bonds from Lys72, Ala80, Ile79, Thr83 and Arg84 to base-pair functional groups can also be formed in our solution structures.

About this Structure

1RCS is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

Reference

The solution structures of the trp repressor-operator DNA complex., Zhang H, Zhao D, Revington M, Lee W, Jia X, Arrowsmith C, Jardetzky O, J Mol Biol. 1994 May 13;238(4):592-614. PMID:8176748 Page seeded by OCA on Sat May 3 07:20:33 2008

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