PDBsum entry 2wv9

Hydrolase

PDB id: 2wv9

Contents

Protein chain

601 a.a. *

Waters ×89

* Residue conservation analysis

PDB id:

2wv9

Name:

Hydrolase

Title:

Crystal structure of the ns3 protease-helicase from murray valley encephalitis virus

Structure:

Flavivirin protease ns2b regulatory subunit, flavivirin protease ns3 catalytic subunit. Chain: a. Fragment: ns2b, residues 1421-1465. Engineered: yes. Other_details: partial polyprotein fragment of ns2b fragment separated from ns3 by a sequence encoding a nine amino acid linker (ggggsgggg).

Source:

Murray valley encephalitis virus. Organism_taxid: 301478. Strain: mve-1-51. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.75Å R-factor: 0.268 R-free: 0.300

Authors:

R.Assenberg,E.Mastrangelo,T.S.Walter,A.Verma,M.Milani,R.J.Owens, D.I.Stuart,J.M.Grimes,E.J.Mancini

Key ref:

R.Assenberg et al. (2009). Crystal structure of a novel conformational state of the flavivirus NS3 protein: implications for polyprotein processing and viral replication. J Virol, 83, 12895-12906. PubMed id: 19793813

Date:

15-Oct-09 Release date: 01-Dec-09

Protein chain

P05769  (POLG_MVEV5) -  Genome polyprotein from Murray valley encephalitis virus (strain MVE-1-51)

Seq: 3434 a.a.

Struc: 601 a.a.*

* PDB and UniProt seqs differ at 19 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.2.1.1.56 - mRNA (guanine-N(7))-methyltransferase.
• Reaction: a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine
• Enzyme class 2: E.C.2.1.1.57 - methyltransferase cap1.
• Reaction: a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H⁺
• Enzyme class 3: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 4: E.C.3.4.21.91 - flavivirin.
• Reaction: Selective hydrolysis of Xaa-Xaa-|-Xbb bonds in which each of the Xaa can be either Arg or Lys and Xbb can be either Ser or Ala.
• Enzyme class 5: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺
• Enzyme class 6: 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 Virol 83:12895-12906 (2009)

PubMed id: 19793813

Crystal structure of a novel conformational state of the flavivirus NS3 protein: implications for polyprotein processing and viral replication.

R.Assenberg, E.Mastrangelo, T.S.Walter, A.Verma, M.Milani, R.J.Owens, D.I.Stuart, J.M.Grimes, E.J.Mancini.

ABSTRACT

The flavivirus genome comprises a single strand of positive-sense RNA, which is translated into a polyprotein and cleaved by a combination of viral and host proteases to yield functional proteins. One of these, nonstructural protein 3 (NS3), is an enzyme with both serine protease and NTPase/helicase activities. NS3 plays a central role in the flavivirus life cycle: the NS3 N-terminal serine protease together with its essential cofactor NS2B is involved in the processing of the polyprotein, whereas the NS3 C-terminal NTPase/helicase is responsible for ATP-dependent RNA strand separation during replication. An unresolved question remains regarding why NS3 appears to encode two apparently disconnected functionalities within one protein. Here we report the 2.75-A-resolution crystal structure of full-length Murray Valley encephalitis virus NS3 fused with the protease activation peptide of NS2B. The biochemical characterization of this construct suggests that the protease has little influence on the helicase activity and vice versa. This finding is in agreement with the structural data, revealing a single protein with two essentially segregated globular domains. Comparison of the structure with that of dengue virus type 4 NS2B-NS3 reveals a relative orientation of the two domains that is radically different between the two structures. Our analysis suggests that the relative domain-domain orientation in NS3 is highly variable and dictated by a flexible interdomain linker. The possible implications of this conformational flexibility for the function of NS3 are discussed.