PDBsum entry 4v0r

Transferase

PDB id: 4v0r

Contents

Protein chain

852 a.a.

Ligands

SAH

GTP

FMT ×3

GOL

Metals

_ZN ×2

_MG ×2

Waters ×406

PDB id:

4v0r

Name:

Transferase

Title:

Dengue virus full length ns5 complexed with gtp and sah

Structure:

Ns5 polymerase. Chain: a. Fragment: unp residues 2494-3385. Engineered: yes

Source:

Dengue virus 3. Organism_taxid: 11069. Strain: singapore strain. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: codon plus.

Resolution:

2.40Å R-factor: 0.190 R-free: 0.237

Authors:

Y.Zhao,S.Soh,J.Zheng,W.W.Phoo,K.Swaminathan,T.C.Cornvik,S.P.Lim,P.- Y.Shi,J.Lescar,S.G.Vasudevan,D.Luo

Key ref:

Y.Zhao et al. (2015). A crystal structure of the Dengue virus NS5 protein reveals a novel inter-domain interface essential for protein flexibility and virus replication. Plos Pathog, 11, e1004682. PubMed id: 25775415 DOI: 10.1371/journal.ppat.1004682

Date:

18-Sep-14 Release date: 28-Jan-15

Protein chain

Q5UB51  (POLG_DEN3I) -  Genome polyprotein from Dengue virus type 3 (strain Singapore/8120/1995)

Seq: 3390 a.a.

Struc: 852 a.a.*

* PDB and UniProt seqs differ at 16 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

5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- methionine = 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine (Bound ligand (Het Group name = SAH) corresponds exactly)

• 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⁺

5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H(+) (Bound ligand (Het Group name = SAH) corresponds exactly)

• 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⁺

ATP (Bound ligand (Het Group name = GTP) matches with 96.88% similarity) + 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

DOI no: 10.1371/journal.ppat.1004682

Plos Pathog 11:e1004682 (2015)

PubMed id: 25775415

A crystal structure of the Dengue virus NS5 protein reveals a novel inter-domain interface essential for protein flexibility and virus replication.

Y.Zhao, T.S.Soh, J.Zheng, K.W.Chan, W.W.Phoo, C.C.Lee, M.Y.Tay, K.Swaminathan, T.C.Cornvik, S.P.Lim, P.Y.Shi, J.Lescar, S.G.Vasudevan, D.Luo.

ABSTRACT

Flavivirus RNA replication occurs within a replication complex (RC) that assembles on ER membranes and comprises both non-structural (NS) viral proteins and host cofactors. As the largest protein component within the flavivirus RC, NS5 plays key enzymatic roles through its N-terminal methyltransferase (MTase) and C-terminal RNA-dependent-RNA polymerase (RdRp) domains, and constitutes a major target for antivirals. We determined a crystal structure of the full-length NS5 protein from Dengue virus serotype 3 (DENV3) at a resolution of 2.3 Å in the presence of bound SAH and GTP. Although the overall molecular shape of NS5 from DENV3 resembles that of NS5 from Japanese Encephalitis Virus (JEV), the relative orientation between the MTase and RdRp domains differs between the two structures, providing direct evidence for the existence of a set of discrete stable molecular conformations that may be required for its function. While the inter-domain region is mostly disordered in NS5 from JEV, the NS5 structure from DENV3 reveals a well-ordered linker region comprising a short 310 helix that may act as a swivel. Solution Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) analysis reveals an increased mobility of the thumb subdomain of RdRp in the context of the full length NS5 protein which correlates well with the analysis of the crystallographic temperature factors. Site-directed mutagenesis targeting the mostly polar interface between the MTase and RdRp domains identified several evolutionarily conserved residues that are important for viral replication, suggesting that inter-domain cross-talk in NS5 regulates virus replication. Collectively, a picture for the molecular origin of NS5 flexibility is emerging with profound implications for flavivirus replication and for the development of therapeutics targeting NS5.