4opk

Bh-RNaseH:2'-SMe-DNA complex

spinqualitylabelsall models 4opk, resolution 1.54Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4opk is a 4 chain structure with sequence from Alkalihalobacillus halodurans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: GOL, USM Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function RNH1_HALH5 Endonuclease that specifically degrades the RNA of RNA-DNA hybrids. Publication Abstract from PubMed The DNA dodecamer 5'-d(CGCGAATTCGCG)-3' is arguably the best studied oligonucleotide and crystal structures of duplexes with this sequence account for a considerable portion of the total number of oligo-2'-deoxynucleotide structures determined over the last 30 years. The dodecamer has commonly served as a template to analyze the effects of sequence on DNA conformation, the conformational properties of chemically modified nucleotides, DNA-ligand interactions as well as water structure and DNA-cation binding. Although molecular replacement is the phasing method of choice given the large number of available models of the dodecamer, this strategy often fails as a result of conformational changes caused by chemical modification, mismatch pairs, or differing packing modes. Here, we describe an alternative approach to determine crystal structures of the dodecamer in cases where molecular replacement does not produce a solution or when crystals of the DNA alone cannot be grown. It is based on the discovery that many dodecamers of the above sequence can be readily co-crystallized with Bacillus halodurans RNase H, whereby the enzyme is unable to cleave the DNA. Determination of the structure of the complex using the protein portion as the search model yields a structural model of the DNA. Provided crystals of the DNA alone are also available, the DNA model from the complex then enables phasing their structures by molecular replacement. Generating Crystallographic Models of DNA Dodecamers from Structures of RNase H:DNA Complexes.,Egli M, Pallan PS Methods Mol Biol. 2016;1320:111-26. doi: 10.1007/978-1-4939-2763-0_8. PMID:26227040 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Ribonuclease 3D structures

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