2p0j
From Proteopedia
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|PDB= 2p0j |SIZE=350|CAPTION= <scene name='initialview01'>2p0j</scene>, resolution 2.100Å | |PDB= 2p0j |SIZE=350|CAPTION= <scene name='initialview01'>2p0j</scene>, resolution 2.100Å | ||
|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= bstYIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus]) | |GENE= bstYIR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1422 Geobacillus stearothermophilus]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1sd0|1SD0]], [[1vrr|1VRR]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2p0j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p0j OCA], [http://www.ebi.ac.uk/pdbsum/2p0j PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2p0j RCSB]</span> | ||
}} | }} | ||
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[[Category: scanning]] | [[Category: scanning]] | ||
| - | ''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 04:26:17 2008'' |
Revision as of 01:26, 31 March 2008
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| , resolution 2.100Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Gene: | bstYIR (Geobacillus stearothermophilus) | ||||||
| Related: | 1SD0, 1VRR
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structure of restriction endonuclease BstYI bound to non-cognate DNA
Overview
DNA recognition by proteins is essential for specific expression of genes in a living organism. En route to a target DNA site, a protein will often sample noncognate DNA sites through nonspecific protein-DNA interactions, resulting in a variety of conformationally different binding states. We present here the crystal structure of endonuclease BstYI bound to a noncognate DNA. Surprisingly, the structure reveals the enzyme in a "hemispecific" binding state on the pathway between nonspecific and specific recognition. A single base pair change in the DNA abolishes binding of only one monomer, with the second monomer bound specifically. We show that the enzyme binds essentially as a rigid body, and that one end of the DNA is accommodated loosely in the binding cleft while the other end is held tightly. Another intriguing feature of the structure is Ser172, which has a dual role in establishing nonspecific and specific contacts. Taken together, the structure provides a snapshot of an enzyme in a "paused" intermediate state that may be part of a more general mechanism of scanning DNA.
About this Structure
2P0J is a Single protein structure of sequence from Geobacillus stearothermophilus. Full crystallographic information is available from OCA.
Reference
BstYI bound to noncognate DNA reveals a "hemispecific" complex: implications for DNA scanning., Townson SA, Samuelson JC, Bao Y, Xu SY, Aggarwal AK, Structure. 2007 Apr;15(4):449-59. PMID:17437717
Page seeded by OCA on Mon Mar 31 04:26:17 2008
