1zrd
From Proteopedia
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|PDB= 1zrd |SIZE=350|CAPTION= <scene name='initialview01'>1zrd</scene>, resolution 2.800Å | |PDB= 1zrd |SIZE=350|CAPTION= <scene name='initialview01'>1zrd</scene>, resolution 2.800Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CMP:ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE'>CMP</scene> | + | |LIGAND= <scene name='pdbligand=CMP:ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE'>CMP</scene>, <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> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= crp, cap, csm ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |GENE= crp, cap, csm ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1zrc|1ZRC]], [[1zre|1ZRE]], [[1zrf|1ZRF]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1zrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zrd OCA], [http://www.ebi.ac.uk/pdbsum/1zrd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1zrd RCSB]</span> | ||
}} | }} | ||
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[[Category: Berman, H M.]] | [[Category: Berman, H M.]] | ||
[[Category: Napoli, A A.]] | [[Category: Napoli, A A.]] | ||
| - | [[Category: CMP]] | ||
[[Category: camp receptor protein]] | [[Category: camp receptor protein]] | ||
[[Category: cap]] | [[Category: cap]] | ||
| Line 32: | Line 34: | ||
[[Category: protein-dna complex]] | [[Category: protein-dna complex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:40:37 2008'' |
Revision as of 22:40, 30 March 2008
| |||||||
| , resolution 2.800Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Gene: | crp, cap, csm (Escherichia coli) | ||||||
| Related: | 1ZRC, 1ZRE, 1ZRF
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
4 crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-[6A;17T]ICAP38 DNA
Overview
The catabolite activator protein (CAP) bends DNA in the CAP-DNA complex, typically introducing a sharp DNA kink, with a roll angle of approximately 40 degrees and a twist angle of approximately 20 degrees, between positions 6 and 7 of the DNA half-site, 5'-A1A2A3T4G5T6G7A8T9C10T11 -3' ("primary kink"). In previous work, we showed that CAP recognizes the nucleotide immediately 5' to the primary-kink site, T6, through an "indirect-readout" mechanism involving sequence effects on energetics of primary-kink formation. Here, to understand further this example of indirect readout, we have determined crystal structures of CAP-DNA complexes containing each possible nucleotide at position 6. The structures show that CAP can introduce a DNA kink at the primary-kink site with any nucleotide at position 6. The DNA kink is sharp with the consensus pyrimidine-purine step T6G7 and the non-consensus pyrimidine-purine step C6G7 (roll angles of approximately 42 degrees, twist angles of approximately 16 degrees ), but is much less sharp with the non-consensus purine-purine steps A6G7 and G6G7 (roll angles of approximately 20 degrees, twist angles of approximately 17 degrees). We infer that CAP discriminates between consensus and non-consensus pyrimidine-purine steps at positions 6-7 solely based on differences in the energetics of DNA deformation, but that CAP discriminates between the consensus pyrimidine-purine step and non-consensus purine-purine steps at positions 6-7 both based on differences in the energetics of DNA deformation and based on qualitative differences in DNA deformation. The structures further show that CAP can achieve a similar, approximately 46 degrees per DNA half-site, overall DNA bend through a sharp DNA kink, a less sharp DNA kink, or a smooth DNA bend. Analysis of these and other crystal structures of CAP-DNA complexes indicates that there is a large, approximately 28 degrees per DNA half-site, out-of-plane component of CAP-induced DNA bending in structures not constrained by end-to-end DNA lattice interactions and that lattice contacts involving CAP tend to involve residues in or near biologically functional surfaces.
About this Structure
1ZRD is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps., Napoli AA, Lawson CL, Ebright RH, Berman HM, J Mol Biol. 2006 Mar 17;357(1):173-83. Epub 2006 Jan 3. PMID:16427082
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