1YN9

Crystal structure of baculovirus RNA 5'-phosphatase complexed with phosphate

Summary for 1YN9

• Entry DOI: 10.2210/pdb1yn9/pdb
• Descriptor: polynucleotide 5'-phosphatase, PHOSPHATE ION (3 entities in total)
• Functional Keywords: rna triphosphatase, cysteine phosphatase, p-loop, hydrolase
• Biological source: Autographa californica nucleopolyhedrovirus
• Total number of polymer chains: 3
• Total formula weight: 58921.17

Authors

Changela, A.,Martins, A.,Shuman, S.,Mondragon, A. (deposition date: 2005-01-24, release date: 2005-02-22, Last modification date: 2023-08-23)

Primary citation

Changela, A.,Martins, A.,Shuman, S.,Mondragon, A.
Crystal structure of baculovirus RNA triphosphatase complexed with phosphate
J.Biol.Chem., 280:17848-17856, 2005

PubMed Abstract: Baculovirus RNA 5'-triphosphatase (BVP) exemplifies a family of RNA-specific cysteine phosphatases that includes the RNA triphosphatase domains of metazoan and plant mRNA capping enzymes. Here we report the crystal structure of BVP in a phosphate-bound state at 1.5 A resolution. BVP adopts the characteristic cysteine-phosphatase alpha/beta fold and binds two phosphate ions in the active site region, one of which is proposed to mimic the phosphate of the product complex after hydrolysis of the covalent phosphoenzyme intermediate. The crystal structure highlights the role of backbone amides and side chains of the P-loop motif (118)HCTHGXNRT(126) in binding the cleavable phosphate and stabilizing the transition state. Comparison of the BVP structure to the apoenzyme of mammalian RNA triphosphatase reveals a concerted movement of the Arg-125 side chain (to engage the phosphate directly) and closure of an associated surface loop over the phosphate in the active site. The structure highlights a direct catalytic role of Asn-124, which is the signature P-loop residue of the RNA triphosphatase family and a likely determinant of the specificity of BVP for hydrolysis of phosphoanhydride linkages.

PubMed: 15713658
DOI: 10.1074/jbc.M500885200

Experimental method

X-RAY DIFFRACTION (1.5 Å)