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Literature summary extracted from
- Atomistic details of the molecular recognition of DNA-RNA hybrid duplex by ribonuclease H enzyme (2015), J. Chem. Sci., 127, 1701-1713 .
No PubMed abstract available
Crystallization (Commentary)
| EC Number | Crystallization (Comment) | Organism |
|---|---|---|
| 3.1.26.4 | Bh ribonuclease H complexed with a DNA-RNA hybrid, PDB ID 1ZBI, modelling, detailed overview | Halalkalibacterium halodurans |
Metals/Ions
| EC Number | Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|---|
| 3.1.26.4 | Mg2+ | required, two Mg2+ ions are located at specific positions in the catalytic site | Halalkalibacterium halodurans |  |
| 3.1.26.4 | Mn2+ | required | Halalkalibacterium halodurans | |
| 3.1.26.4 | additional information | the enzyme uses two-metal ion (Mg2+ or Mn2+) catalysis to cleave nucleic acids | Halalkalibacterium halodurans |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 3.1.26.4 | Halalkalibacterium halodurans | Q9KEI9 | - |
- |
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 3.1.26.4 | additional information | conformational changes upon DNA-RNA hybrid duplex substrate binding, overview | Halalkalibacterium halodurans | ? | - |
? | |
Subunits
| EC Number | Subunits | Comment | Organism |
|---|---|---|---|
| 3.1.26.4 | More | secondary enzyme structure analysis, overview. Structures and dynamics of apo state of the RNase H enzyme and DNA-RNA hybrid | Halalkalibacterium halodurans |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 3.1.26.4 | Bh ribonuclease H | - |
Halalkalibacterium halodurans |
| 3.1.26.4 | BhRNase H | - |
Halalkalibacterium halodurans |
| 3.1.26.4 | ribonuclease H | - |
Halalkalibacterium halodurans |
| 3.1.26.4 | rnhA | - |
Halalkalibacterium halodurans |
General Information
| EC Number | General Information | Comment | Organism |
|---|---|---|---|
| 3.1.26.4 | evolution | ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and is a prototypical member of a large family of enzymes that use two-metal ion (Mg2+ or Mn2+) catalysis to cleave nucleic acids | Halalkalibacterium halodurans |
| 3.1.26.4 | additional information | atomistic details of the molecular recognition of DNA-RNA hybrid duplex by ribonuclease H enzyme, overview. The beta1 strand of the protein interacts with the DNA-RNA hybrid. Long timescale molecular dynamics simulations are performed on the BhRNase H-DNA-RNA hybrid complex and the respective monomers, analysis of recognition mechanism, conformational preorganization, active site dynamics and energetics involved in the complex formation, overview. The active site region contains three aspartic acids (D10, D71 and D131) and two glutamic acids (E48 and E127) along with two Mg2+ ions and water molecules, active site dynamics. The ability of the DNA strand in the hybrid duplex to sample conformations corresponding to typical A- and B-type nucleic acids and the characteristic minor groove width seem to be crucial for efficient binding. Sugar moieties in certain positions interacting with the protein structure undergo notable conformational transitions. The water coordination and arrangement around the metal ions in active site region are quite stable, suggesting their important role in enzymatic catalysis. Key interactions located at the interface of enzyme-nucleic acid complex are responsible for its stability | Halalkalibacterium halodurans |
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