PDBsum entry 2r7t

Transferase/RNA

PDB id

2r7t

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Contents

			Protein chain

					1073 a.a. *

			DNA/RNA

* Residue conservation analysis

PDB id:

2r7t

Links

Name:

Transferase/RNA

Title:

Crystal structure of rotavirus sa11 vp1/RNA (ugugaacc) complex

Structure:

RNA (5'-r( Up Gp Up Gp Ap Ap Cp C)-3'). Chain: x. Engineered: yes. RNA-dependent RNA polymerase. Chain: a. Engineered: yes

Source:

Synthetic: yes. Simian rotavirus. Organism_taxid: 10922. Strain: sa11. Gene: gene 1. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108.

Resolution:

3.00Å

R-factor:

0.235

R-free:

0.280

Authors:

X.Lu,S.C.Harrison,Y.J.Tao,J.T.Patton,M.L.Nibert

Key ref:

X.Lu et al. (2008). Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1. Structure, 16, 1678-1688. PubMed id: 19000820

Date:

10-Sep-07

Release date:

29-Jul-08

PROCHECK

	Headers

	References

Protein chain

O37061 (RDRP_ROTSP) - RNA-directed RNA polymerase from Rotavirus A (strain RVA/SA11-Patton/G3P[X])

Seq: Struc:

Seq: Struc:

Seq: Struc:					1088 a.a. 1073 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

DNA/RNA chain

U-G-U-G-A-A-C 7 bases



		Enzyme reactions

Enzyme class:

E.C.2.7.7.48 - RNA-directed Rna polymerase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

RNA(n)	+	ribonucleoside 5'-triphosphate	=	RNA(n+1)	+	diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

	Structure 16:1678-1688 (2008)
PubMed id: 19000820

Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1.
X.Lu, S.M.McDonald, M.A.Tortorici, Y.J.Tao, R.Vasquez-Del Carpio, M.L.Nibert, J.T.Patton, S.C.Harrison.

ABSTRACT

Rotavirus RNA-dependent RNA polymerase VP1 catalyzes RNA synthesis within a subviral particle. This activity depends on core shell protein VP2. A conserved sequence at the 3' end of plus-strand RNA templates is important for polymerase association and genome replication. We have determined the structure of VP1 at 2.9 A resolution, as apoenzyme and in complex with RNA. The cage-like enzyme is similar to reovirus lambda3, with four tunnels leading to or from a central, catalytic cavity. A distinguishing characteristic of VP1 is specific recognition, by conserved features of the template-entry channel, of four bases, UGUG, in the conserved 3' sequence. Well-defined interactions with these bases position the RNA so that its 3' end overshoots the initiating register, producing a stable but catalytically inactive complex. We propose that specific 3' end recognition selects rotavirus RNA for packaging and that VP2 activates the autoinhibited VP1/RNA complex to coordinate packaging and genome replication.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21195621

S.M.McDonald, and J.T.Patton (2011).
Assortment and packaging of the segmented rotavirus genome.

Trends Microbiol, 19, 136-144.

20122940

B.McClain, E.Settembre, B.R.Temple, A.R.Bellamy, and S.C.Harrison (2010).
X-ray crystal structure of the rotavirus inner capsid particle at 3.8 A resolution.

J Mol Biol, 397, 587-599.

PDB code:

3kz4

20479224

S.L.Noton, V.M.Cowton, C.R.Zack, D.R.McGivern, and R.Fearns (2010).
Evidence that the polymerase of respiratory syncytial virus initiates RNA replication in a nontemplated fashion.

Proc Natl Acad Sci U S A, 107, 10226-10231.

20671030

W.Li, E.Manktelow, J.C.von Kirchbach, J.R.Gog, U.Desselberger, and A.M.Lever (2010).
Genomic analysis of codon, sequence and structural conservation with selective biochemical-structure mapping reveals highly conserved and dynamic structures in rotavirus RNAs with potential cis-acting functions.

Nucleic Acids Res, 38, 7718-7735.

19297468

A.A.Demidenko, and M.L.Nibert (2009).
Probing the transcription mechanisms of reovirus cores with molecules that alter RNA duplex stability.

J Virol, 83, 5659-5670.

19357162

S.M.McDonald, D.Aguayo, F.D.Gonzalez-Nilo, and J.T.Patton (2009).
Shared and group-specific features of the rotavirus RNA polymerase reveal potential determinants of gene reassortment restriction.

J Virol, 83, 6135-6148.

19000811

A.Shatkin, K.Das, and E.Arnold (2008).
3D jigsaw puzzle in rotavirus assembly.

Structure, 16, 1601-1602.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.