3DD6

Crystal structure of Rph, an exoribonuclease from Bacillus anthracis at 1.7 A resolution

Summary for 3DD6

• Entry DOI: 10.2210/pdb3dd6/pdb
• Descriptor: Ribonuclease PH, SULFATE ION (3 entities in total)
• Functional Keywords: exoribonuclease, bacillus anthracis, trna maturation, rnase ph., transferase, structural genomics, structural proteomics in europe 2, spine-2
• Biological source: Bacillus anthracis
• Total number of polymer chains: 1
• Total formula weight: 28687.41

Authors

Rawlings, A.E.,Blagova, E.V.,Levdikov, V.M.,Fogg, M.J.,Wilson, K.S.,Wilkinson, A.J.,Structural Proteomics in Europe 2 (SPINE-2) (deposition date: 2008-06-05, release date: 2009-02-10, Last modification date: 2023-08-30)

Primary citation

Rawlings, A.E.,Blagova, E.V.,Levdikov, V.M.,Fogg, M.J.,Wilson, K.S.,Wilkinson, A.J.
The structure of Rph, an exoribonuclease from Bacillus anthracis, at 1.7 A resolution.
Acta Crystallogr.,Sect.F, 65:2-7, 2009

PubMed Abstract: Maturation of tRNA precursors into functional tRNA molecules requires trimming of the primary transcript at both the 5' and 3' ends. Cleavage of nucleotides from the 3' stem of tRNA precursors, releasing nucleotide diphosphates, is accomplished in Bacillus by a phosphate-dependent exoribonuclease, Rph. The crystal structure of this enzyme from B. anthracis has been solved by molecular replacement to a resolution of 1.7 A and refined to an R factor of 19.3%. There is one molecule in the asymmetric unit; the crystal packing reveals the assembly of the protein into a hexamer arranged as a trimer of dimers. The structure shows two sulfate ions bound in the active-site pocket, probably mimicking the phosphate substrate and the phosphate of the 3'-terminal nucleotide of the tRNA precursor. Three other bound sulfate ions point to likely RNA-binding sites.

PubMed: 19153445
DOI: 10.1107/S1744309108041511

Experimental method

X-RAY DIFFRACTION (1.702 Å)