4hug | pdb_00004hug

Structure of 5-chlorouracil modified A:U base pairs

spinqualitylabelsall models 4hug, resolution 1.64Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4hug is a 6 chain structure with sequence from Alkalihalobacillus halodurans C-125. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: EDO, GOL, MG, UCL 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 thymine analog 5-chlorouridine, first reported in the 1950s as anti-tumor agent, is known as an effective mutagen, clastogen and toxicant as well as an effective inducer of sister-chromatid exchange. Recently, the first microorganism with a chemically different genome was reported; the selected Escherichia coli strain relies on the four building blocks 5-chloro-2'-deoxyuridine (ClU), A, C and G instead of the standard T, A, C, G alphabet [Marliere,P., Patrouix,J., Doring,V., Herdewijn,P., Tricot,S., Cruveiller,S., Bouzon,M. and Mutzel,R. (2011) Chemical evolution of a bacterium's genome. Angew. Chem. Int. Ed., 50, 7109-7114]. The residual fraction of T in the DNA of adapted bacteria was <2% and the switch from T to ClU was accompanied by a massive number of mutations, including >1500 A to G or G to A transitions in a culture. The former is most likely due to wobble base pairing between ClU and G, which may be more common for ClU than T. To identify potential changes in the geometries of base pairs and duplexes as a result of replacement of T by ClU, we determined four crystal structures of a B-form DNA dodecamer duplex containing ClU:A or ClU:G base pairs. The structures reveal nearly identical geometries of these pairs compared with T:A or T:G, respectively, and no consequences for stability and cleavage by an endonuclease (EcoRI). The lack of significant changes in the geometry of ClU:A and ClU:G base pairs relative to the corresponding native pairs is consistent with the sustained unlimited self-reproduction of E. coli strains with virtually complete T-->ClU genome substitution. Structure, stability and function of 5-chlorouracil modified A:U and G:U base pairs.,Patra A, Harp J, Pallan PS, Zhao L, Abramov M, Herdewijn P, Egli M Nucleic Acids Res. 2012 Dec 28. PMID:23275540 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Ribonuclease 3D structures

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