PDBsum entry 3o8c

Hydrolase/RNA

PDB id: 3o8c

Contents

Protein chains

645 a.a.

DNA/RNA

Ligands

SO4 ×2

Metals

_ZN ×2

Waters ×796

PDB id:

3o8c

Name:

Hydrolase/RNA

Title:

Visualizing atp-dependent RNA translocation by the ns3 helicase from hcv

Structure:

Hcv ns3 protease/helicase. Chain: a, b. Engineered: yes. RNA (5'-r(p Up (5Bu)p Up Up Up U)-3'). Chain: c. Engineered: yes

Source:

Hepatitis c virus subtype 1b. Organism_taxid: 31647. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: this oligonucleotide was created with an automated RNA/DNA synthesizer using phosphoramidite chemistry.

Resolution:

2.00Å R-factor: 0.200 R-free: 0.232

Authors:

T.C.Appleby,J.R.Somoza

Key ref:

T.C.Appleby et al. (2011). Visualizing ATP-dependent RNA translocation by the NS3 helicase from HCV. J Mol Biol, 405, 1139-1153. PubMed id: 21145896

Date:

02-Aug-10 Release date: 05-Jan-11

Protein chains

Q99AU2  (Q99AU2_9HEPC) -  Genome polyprotein from Hepatitis C virus subtype 1b

Seq: 3010 a.a.

Struc: 645 a.a.*

* PDB and UniProt seqs differ at 15 residue positions (black crosses)

DNA/RNA chain

U-5BU-U-U-U-U 6 bases

Enzyme reactions

• Enzyme class 1: E.C.3.4.21.98 - hepacivirin.
• Reaction: Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
• Enzyme class 2: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺
• Enzyme class 3: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + 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 Mol Biol 405:1139-1153 (2011)

PubMed id: 21145896

Visualizing ATP-dependent RNA translocation by the NS3 helicase from HCV.

T.C.Appleby, R.Anderson, O.Fedorova, A.M.Pyle, R.Wang, X.Liu, K.M.Brendza, J.R.Somoza.

ABSTRACT

The structural mechanism by which nonstructural protein 3 (NS3) from the hepatitis C virus (HCV) translocates along RNA is currently unknown. HCV NS3 is an ATP-dependent motor protein essential for viral replication and a member of the superfamily 2 helicases. Crystallographic analysis using a labeled RNA oligonucleotide allowed us to unambiguously track the positional changes of RNA bound to full-length HCV NS3 during two discrete steps of the ATP hydrolytic cycle. The crystal structures of HCV NS3, NS3 bound to bromine-labeled RNA, and a tertiary complex of NS3 bound to labeled RNA and a non-hydrolyzable ATP analog provide a direct view of how large domain movements resulting from ATP binding and hydrolysis allow the enzyme to translocate along the phosphodiester backbone. While directional translocation of HCV NS3 by a single base pair per ATP hydrolyzed is observed, the 3' end of the RNA does not shift register with respect to a conserved tryptophan residue, supporting a "spring-loading" mechanism that leads to larger steps by the enzyme as it moves along a nucleic acid substrate.