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Literature summary extracted from

  • Davis, R.R.; Shaban, N.M.; Perrino, F.W.; Hollis, T.
    Crystal structure of RNA-DNA duplex provides insight into conformational changes induced by RNase H binding (2015), Cell Cycle, 14, 668-673 .
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.1.26.4 annealed RNA and DNA dodecanucleotides complexed with RNase H, synthetic constructs, sitting drop vapor diffusion method at room temperature in conditions containing 20% PEG 3350, 0.2 M magnesium formate, 10% 2-methyl-2,4-pentanediol, X-ray diffraction structure determination and analysis, molecular replacement using the structure of Bacillus halodurans RNA-DNA component of the RNase H complex (PDB ID 1ZBI) as the search model Halalkalibacterium halodurans

Organism

EC Number Organism UniProt Comment Textmining
3.1.26.4 Halalkalibacterium halodurans
-
 and synthetic constructs
-
3.1.26.4 Halalkalibacterium halodurans C-125
-
 and synthetic constructs
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.1.26.4 additional information RNase (H)binding induces conformational changes in RNA-DNA hybrid. RNase H distorts the DNA strand of the hybrid by rotating the phosphodiester backbone around nucleotide dA6 about 5 A x02into the nucleotide binding pocket. The superimposition of the 2 RNA-DNA hybrids shows the RNA strand has a relatively similar conformation, but the DNA strand has been distorted to significantly widen the major groove of the helix. This flexibility of the DNA strand likely plays a role in substrate recognition and discrimination Halalkalibacterium halodurans ?
-
 ?
3.1.26.4 additional information RNase (H)binding induces conformational changes in RNA-DNA hybrid. RNase H distorts the DNA strand of the hybrid by rotating the phosphodiester backbone around nucleotide dA6 about 5 A x02into the nucleotide binding pocket. The superimposition of the 2 RNA-DNA hybrids shows the RNA strand has a relatively similar conformation, but the DNA strand has been distorted to significantly widen the major groove of the helix. This flexibility of the DNA strand likely plays a role in substrate recognition and discrimination Halalkalibacterium halodurans C-125 ?
-
 ?

Synonyms

EC Number Synonyms Comment Organism
3.1.26.4 RNase H
-
 Halalkalibacterium halodurans

General Information

EC Number General Information Comment Organism
3.1.26.4 additional information conformational changes induced by RNase H binding of RNA:DNA heteroduplexes, crystal structure analysis of a dodecameric nonpolypurine/polypyrimidine tract RNA-DNA duplex and of the same sequence bound to RNase H, overview. The structural changes to the duplex include widening of the major groove to 12.5 A from 4.2 A and decrease in the degree of bending along the axis which may play a crucial role in the ribonucleotide recognition and cleavage mechanism within RNase H Halalkalibacterium halodurans
3.1.26.4 physiological function ribonucleotides within RNA-DNA hybrids are recognized and hydrolyzed by the RNase H enzymes Halalkalibacterium halodurans