PDBsum entry 1khv

Transferase

PDB id: 1khv

Contents

Protein chains

493 a.a. *

Metals

_LU ×2

Waters ×161

* Residue conservation analysis

PDB id:

1khv

Name:

Transferase

Title:

Crystal structure of rabbit hemorrhagic disease virus RNA-dependent RNA polymerase complexed with lu3+

Structure:

RNA-directed RNA polymerase. Chain: a, b. Fragment: (residues 1252-1767). Synonym: RNA-dependent RNA polymerase. Engineered: yes

Source:

Rabbit hemorrhagic disease virus. Organism_taxid: 11976. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.50Å R-factor: 0.218 R-free: 0.265

Authors:

K.K.Ng,M.M.Cherney,A.L.Vazquez,A.Machin,J.M.Alonso,F.Parra,M.N.James

Key ref:

K.K.Ng et al. (2002). Crystal structures of active and inactive conformations of a caliciviral RNA-dependent RNA polymerase. J Biol Chem, 277, 1381-1387. PubMed id: 11677245 DOI: 10.1074/jbc.M109261200

Date:

01-Dec-01 Release date: 16-Jan-02

Protein chains

P27410  (POLG_RHDVF) -  Genome polyprotein from Rabbit hemorrhagic disease virus (strain Rabbit/Germany/FRG/1989)

Seq: 2344 a.a.

Struc: 493 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 2: E.C.3.4.22.66 - calicivirin.
• Enzyme class 3: 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: 10.1074/jbc.M109261200

J Biol Chem 277:1381-1387 (2002)

PubMed id: 11677245

Crystal structures of active and inactive conformations of a caliciviral RNA-dependent RNA polymerase.

K.K.Ng, M.M.Cherney, A.L.Vazquez, A.Machin, J.M.Alonso, F.Parra, M.N.James.

ABSTRACT

The structure of the RNA-dependent RNA polymerase (RdRP) from the rabbit hemorrhagic disease virus has been determined by x-ray crystallography to a 2.5-A resolution. The overall structure resembles a "right hand," as seen before in other polymerases, including the RdRPs of polio virus and hepatitis C virus. Two copies of the polymerase are present in the asymmetric unit of the crystal, revealing active and inactive conformations within the same crystal form. The fingers and palm domains form a relatively rigid unit, but the thumb domain can adopt either "closed" or "open" conformations differing by a rigid body rotation of approximately 8 degrees. Metal ions bind at different positions in the two conformations and suggest how structural changes may be important to enzymatic function in RdRPs. Comparisons between the structures of the alternate conformational states of rabbit hemorrhagic disease virus RdRP and the structures of RdRPs from hepatitis C virus and polio virus suggest novel structure-function relationships in this medically important class of enzymes.

Selected figure(s)

Figure 2.
Fig. 2. Ribbon diagrams of RNA-dependent RNA polymerases shown from a similar vantage point. A, RHDV; B, PV (PDB code 1RDR) (8); and C, HCV (PDB code 1C2P) (11). Side chains of active site aspartic acid residues (Asp-250 and Asp-354 in RHDV) are drawn as balls and sticks, and Mn2+ ions are drawn as pink spheres. The Ca^2+ ion found near the active site in the polio virus structure is drawn as a gray sphere. There were no bound metal ions reported in the HCV RdRP structures.

Figure 3.
Fig. 3. Conformational differences between two copies in the asymmetric unit of RHDV RdRP (Lu3+ cocrystal structure, stereoscopic view). Copy A is colored in red, and copy B is colored in blue. The palm and fingers domains were superposed to emphasize the movement of the thumb and N-terminal domains relative to the central core of the protein.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 1381-1387) copyright 2002.

Figures were selected by an automated process.