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1rta
From Proteopedia
| 1rta, resolution 2.50Å () | |||||||||
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| Activity: | Pancreatic ribonuclease, with EC number 3.1.27.5 | ||||||||
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
Crystal structure disposition of thymidic acid tetramer in complex with ribonuclease A
Active Site
Ribonuclease A cleaves RNA strands by catalyzing a transphosphorylation reaction where the 2'-OH of the ribose sugar attacks the neighboring phosphate, releasing the ribose on the the other side of the phosphate. This structure shows ribonuclease A (in blue) bound to short DNA strand composed of four thymidines (in pink). Ribonuclease binds tightly to DNA, but since DNA is missing the 2'-OH, ribonuclease does not cleave it. are shown that are important for catalysis. The 3' carbon on the DNA is shown in red--it is the site where the 2'-OH is connected in RNA. The two histidines perform the proton transfers that are needed in the reaction, and the lysine stabilizes the intermediate that is formed as the 2'-OH attacks the phosphate. Ribonuclease cleaves RNA strands best next to cytidine and uridine nucleotides--the reason for this may be seen in a . Notice that the small pyrimidine base is surrounded by protein atoms. A larger purine base would not fit well in this space.
This section complements the article on Ribonuclease A in the Molecule of the Month Series. See also Teaching Scenes, Tutorials, and Educators' Pages.
The crystal structure of ribonuclease A with bound thymidylic acid tetramer is reported at 2.5-A resolution. The diffusion of the tetramer into native orthorhombic crystals of the ribonuclease allows for the formation of a structurally stable complex where the single-stranded nucleic acid enters and leaves the enzyme's catalytic region in a persistent 5'-3' direction. The binding of the tetramer to the enzyme's surface is facilitated and mediated by electrostatic interactions between basic protein residues and nucleotide phosphates. Two pyrimidine nucleotides are bound to the enzyme's active site in a manner similar to that observed for other complexes between ribonuclease A and nucleic acid oligomers.
Crystal structure disposition of thymidylic acid tetramer in complex with ribonuclease A., Birdsall DL, McPherson A, J Biol Chem. 1992 Nov 5;267(31):22230-6. PMID:1429575
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
About this Structure
1RTA is a Single protein structure of sequence from Bos taurus. The September 2008 Molecule of the Month feature on Ribonuclease A by David Goodsell is http://dx.doi.org/10.2210/rcsb_pdb/mom_2008_9. Full crystallographic information is available from OCA.
Reference
Crystal structure disposition of thymidylic acid tetramer in complex with ribonuclease A., Birdsall DL, McPherson A, J Biol Chem. 1992 Nov 5;267(31):22230-6. PMID:1429575
Page seeded by OCA on Mon Jul 28 17:53:34 2008
Proteopedia Page Contributors and Editors (what is this?)
OCA, David S. Goodsell, Jaime Prilusky, Eran Hodis, Eric Martz
