PDBsum entry 2r7c

RNA binding protein

PDB id: 2r7c

Contents

Protein chain

308 a.a. *

Ligands

PO4

Waters ×15

* Residue conservation analysis

PDB id:

2r7c

Name:

RNA binding protein

Title:

Crystallographic and biochemical analysis of rotavirus nsp2 with nucleotides reveals an ndp kinase like activity

Structure:

Non-structural RNA-binding protein 35. Chain: a. Synonym: nsp2, ns35, ncvp3. Engineered: yes

Source:

Simian 11 rotavirus (serotype 3 / strain sa11- ramig). Organism_taxid: 36435. Strain: ramig. Gene: s8, segment 8. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.70Å R-factor: 0.226 R-free: 0.278

Authors:

M.Kumar,B.V.V.Prasad

Key ref:

M.Kumar et al. (2007). Crystallographic and biochemical analysis of rotavirus NSP2 with nucleotides reveals a nucleoside diphosphate kinase-like activity. J Virol, 81, 12272-12284. PubMed id: 17804496

Date:

07-Sep-07 Release date: 23-Oct-07

Protein chain

Q03243  (NSP2_ROTSR) -  Non-structural protein 2 from Rotavirus A (strain RVA/SA11-Ramig/G3P[X])

Seq: 317 a.a.

Struc: 308 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.6.4.- - ?????

J Virol 81:12272-12284 (2007)

PubMed id: 17804496

Crystallographic and biochemical analysis of rotavirus NSP2 with nucleotides reveals a nucleoside diphosphate kinase-like activity.

M.Kumar, H.Jayaram, R.Vasquez-Del Carpio, X.Jiang, Z.F.Taraporewala, R.H.Jacobson, J.T.Patton, B.V.Prasad.

ABSTRACT

Rotavirus, the major pathogen of infantile gastroenteritis, carries a nonstructural protein, NSP2, essential for viroplasm formation and genome replication/packaging. In addition to RNA-binding and helix-destabilizing properties, NSP2 exhibits nucleoside triphosphatase activity. A conserved histidine (H225) functions as the catalytic residue for this enzymatic activity, and mutation of this residue abrogates genomic double-stranded RNA synthesis without affecting viroplasm formation. To understand the structural basis of the phosphatase activity of NSP2, we performed crystallographic analyses of native NSP2 and a functionally defective H225A mutant in the presence of nucleotides. These studies showed that nucleotides bind inside a cleft between the two domains of NSP2 in a region that exhibits structural similarity to ubiquitous cellular HIT (histidine triad) proteins. Only minor conformational alterations were observed in the cleft upon nucleotide binding and hydrolysis. This hydrolysis involved the formation of a stable phosphohistidine intermediate. These observations, reminiscent of cellular nucleoside diphosphate (NDP) kinases, prompted us to investigate whether NSP2 exhibits phosphoryl-transfer activity. Bioluminometric assay showed that NSP2 exhibits an NDP kinase-like activity that transfers the bound phosphate to NDPs. However, NSP2 is distinct from the highly conserved cellular NDP kinases in both its structure and catalytic mechanism, thus making NSP2 a potential target for antiviral drug design. With structural similarities to HIT proteins, which are not known to exhibit NDP kinase activity, NSP2 represents a unique example among structure-activity relationships. The newly observed phosphoryl-transfer activity of NSP2 may be utilized for homeostasis of nucleotide pools in viroplasms during genome replication.