1rcs
From Proteopedia
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|PDB= 1rcs |SIZE=350|CAPTION= <scene name='initialview01'>1rcs</scene> | |PDB= 1rcs |SIZE=350|CAPTION= <scene name='initialview01'>1rcs</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene> | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=TRP:TRYPTOPHAN'>TRP</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |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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[[Category: Zhao, D.]] | [[Category: Zhao, D.]] | ||
[[Category: Zheng, Z.]] | [[Category: Zheng, Z.]] | ||
| - | [[Category: TRP]] | ||
[[Category: dna]] | [[Category: dna]] | ||
[[Category: dna-binding]] | [[Category: dna-binding]] | ||
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[[Category: trp]] | [[Category: trp]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:26:18 2008'' |
Revision as of 20:26, 30 March 2008
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| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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 Sun Mar 30 23:26:18 2008
Categories: Escherichia coli | Single protein | Zhao, D. | Zheng, Z. | Dna | Dna-binding | Peptide | Repressor | Transcription regulation | Trp
