PDBsum entry 1tp7

Transferase

PDB id: 1tp7

Contents

Protein chains

460 a.a. *

Ligands

SO4 ×4

DMX

Waters ×270

* Residue conservation analysis

PDB id:

1tp7

Name:

Transferase

Title:

Crystal structure of the RNA-dependent RNA polymerase from human rhinovirus 16

Structure:

Genome polyprotein. Chain: a, b, c, d. Fragment: RNA-directed RNA polymerase (residues 1694-2153). Synonym: p3d. Engineered: yes

Source:

Human rhinovirus 16. Organism_taxid: 31708. Gene: 3d. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.40Å R-factor: 0.243 R-free: 0.292

Authors:

T.C.Appleby,H.Luecke,J.H.Shim,J.Z.Wu,I.W.Cheney,W.Zhong,L.Vogeley, Z.Hong,N.Yao

Key ref:

T.C.Appleby et al. (2005). Crystal structure of complete rhinovirus RNA polymerase suggests front loading of protein primer. J Virol, 79, 277-288. PubMed id: 15596823

Date:

15-Jun-04 Release date: 21-Jun-05

Protein chains

Q82122  (POLG_HRV16) -  Genome polyprotein from Human rhinovirus 16

Seq: 2153 a.a.

Struc: 460 a.a.

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

J Virol 79:277-288 (2005)

PubMed id: 15596823

Crystal structure of complete rhinovirus RNA polymerase suggests front loading of protein primer.

T.C.Appleby, H.Luecke, J.H.Shim, J.Z.Wu, I.W.Cheney, W.Zhong, L.Vogeley, Z.Hong, N.Yao.

ABSTRACT

Picornaviruses utilize virally encoded RNA polymerase and a uridylylated protein primer to ensure replication of the entire viral genome. The molecular details of this mechanism are not well understood due to the lack of structural information. We report the crystal structure of human rhinovirus 16 3D RNA-dependent RNA polymerase (HRV16 3Dpol) at a 2.4-A resolution, representing the first complete polymerase structure from the Picornaviridae family. HRV16 3Dpol shares the canonical features of other known polymerase structures and contains an N-terminal region that tethers the fingers and thumb subdomains, forming a completely encircled active site cavity which is accessible through a small tunnel on the backside of the molecule. The small thumb subdomain contributes to the formation of a large cleft on the front face of the polymerase which also leads to the active site. The cleft appears large enough to accommodate a template:primer duplex during RNA elongation or a protein primer during the uridylylation stage of replication initiation. Based on the structural features of HRV16 3Dpo1 and the catalytic mechanism known for all polymerases, a front-loading model for uridylylation is proposed.