PDBsum entry 1xr6

Transferase

PDB id: 1xr6

Contents

Protein chain

460 a.a. *

Metals

__K

Waters ×251

* Residue conservation analysis

PDB id:

1xr6

Name:

Transferase

Title:

Crystal structure of RNA-dependent RNA polymerase 3d from human rhinovirus serotype 1b

Structure:

Genome polyprotein. Chain: a. Fragment: RNA-directed RNA polymerase. Engineered: yes

Source:

Human rhinovirus 1b. Organism_taxid: 12129. Gene: p3d. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Other_details: t7 promoter

Resolution:

2.50Å R-factor: 0.230 R-free: 0.263

Authors:

R.A.Love,K.A.Maegley,X.Yu,R.A.Ferre,L.K.Lingardo,W.Diehl,H.E.Parge, P.S.Dragovich,S.A.Fuhrman

Key ref:

R.A.Love et al. (2004). The crystal structure of the RNA-dependent RNA polymerase from human rhinovirus: a dual function target for common cold antiviral therapy. Structure, 12, 1533-1544. PubMed id: 15296746 DOI: 10.1016/j.str.2004.05.024

Date:

13-Oct-04 Release date: 26-Oct-04

Supersedes:

1te8

Protein chain

P12916  (POLG_HRV1B) -  Genome polyprotein from Human rhinovirus 1B

Seq: 2157 a.a.

Struc: 460 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 3: E.C.3.4.22.28 - picornain 3C.
• Reaction: Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
• Enzyme class 4: E.C.3.4.22.29 - picornain 2A.
• Reaction: Selective cleavage of Tyr-|-Gly bond in the picornavirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
• Enzyme class 5: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1016/j.str.2004.05.024

Structure 12:1533-1544 (2004)

PubMed id: 15296746

The crystal structure of the RNA-dependent RNA polymerase from human rhinovirus: a dual function target for common cold antiviral therapy.

R.A.Love, K.A.Maegley, X.Yu, R.A.Ferre, L.K.Lingardo, W.Diehl, H.E.Parge, P.S.Dragovich, S.A.Fuhrman.

ABSTRACT

Human rhinoviruses (HRV), the predominant members of the Picornaviridae family of positive-strand RNA viruses, are the major causative agents of the common cold. Given the lack of effective treatments for rhinoviral infections, virally encoded proteins have become attractive therapeutic targets. The HRV genome encodes an RNA-dependent RNA polymerase (RdRp) denoted 3Dpol, which is responsible for replicating the viral genome and for synthesizing a protein primer used in the replication. Here the crystal structures for three viral serotypes (1B, 14, and 16) of HRV 3Dpol have been determined. The three structures are very similar to one another, and to the closely related poliovirus (PV) 3Dpol enzyme. Because the reported PV crystal structure shows significant disorder, HRV 3Dpol provides the first complete view of a picornaviral RdRp. The folding topology of HRV 3Dpol also resembles that of RdRps from hepatitis C virus (HCV) and rabbit hemorrhagic disease virus (RHDV) despite very low sequence homology.

Selected figure(s)

Figure 1.
Figure 1. Experimental Density Map for HRV 3D^polStereoview of the 2.8 Å SAD electron density map for HRV14 3D^pol in the vicinity of the active site (contoured at 2s), derived from SHARP using the anomalous signal of bound samarium (red sphere). The refined structure of HRV14 3D^pol is superimposed.

The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 1533-1544) copyright 2004.

Figure was selected by an automated process.