1bdt: Difference between revisions
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|PDB= 1bdt |SIZE=350|CAPTION= <scene name='initialview01'>1bdt</scene>, resolution 2.5Å | |PDB= 1bdt |SIZE=350|CAPTION= <scene name='initialview01'>1bdt</scene>, resolution 2.5Å | ||
|SITE= | |SITE= | ||
|LIGAND= | |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> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bdt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bdt OCA], [http://www.ebi.ac.uk/pdbsum/1bdt PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1bdt RCSB]</span> | |||
}} | }} | ||
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==About this Structure== | ==About this Structure== | ||
1BDT is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/ | 1BDT is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_p22 Enterobacteria phage p22]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BDT OCA]. | ||
==Reference== | ==Reference== | ||
Origins of DNA-binding specificity: role of protein contacts with the DNA backbone., Schildbach JF, Karzai AW, Raumann BE, Sauer RT, Proc Natl Acad Sci U S A. 1999 Feb 2;96(3):811-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9927650 9927650] | Origins of DNA-binding specificity: role of protein contacts with the DNA backbone., Schildbach JF, Karzai AW, Raumann BE, Sauer RT, Proc Natl Acad Sci U S A. 1999 Feb 2;96(3):811-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9927650 9927650] | ||
[[Category: Enterobacteria phage p22]] | |||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Karzai, A W.]] | [[Category: Karzai, A W.]] | ||
[[Category: Raumann, B E.]] | [[Category: Raumann, B E.]] | ||
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[[Category: gene-regulating protein]] | [[Category: gene-regulating protein]] | ||
''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 18:58:50 2008'' | ||
Revision as of 18:58, 30 March 2008
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| , resolution 2.5Å | |||||||
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| Ligands: | , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
WILD TYPE GENE-REGULATING PROTEIN ARC/DNA COMPLEX
OverviewOverview
A central question in protein-DNA recognition is the origin of the specificity that permits binding to the correct site in the presence of excess, nonspecific DNA. In the P22 Arc repressor, the Phe-10 side chain is part of the hydrophobic core of the free protein but rotates out to pack against the sugar-phosphate backbone of the DNA in the repressor-operator complex. Characterization of a library of position 10 variants reveals that Phe is the only residue that results in fully active Arc. One class of mutants folds stably but binds operator with reduced affinity; another class is unstable. FV10, one member of the first class, binds operator DNA and nonoperator DNA almost equally well. The affinity differences between FV10 and wild type indicate that each Phe-10 side chain contributes 1.5-2.0 kcal to operator binding but less than 0.5 kcal/mol to nonoperator binding, demonstrating that contacts between Phe-10 and the operator DNA backbone contribute to binding specificity. This appears to be a direct contribution as the crystal structure of the FV10 dimer is similar to wild type and the Phe-10-DNA backbone interactions are the only contacts perturbed in the cocrystal structure of the FV10-operator complex.
About this StructureAbout this Structure
1BDT is a Single protein structure of sequence from Enterobacteria phage p22. Full crystallographic information is available from OCA.
ReferenceReference
Origins of DNA-binding specificity: role of protein contacts with the DNA backbone., Schildbach JF, Karzai AW, Raumann BE, Sauer RT, Proc Natl Acad Sci U S A. 1999 Feb 2;96(3):811-7. PMID:9927650
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